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1638 result(s) for 'natural language processing' within BMC Bioinformatics

Page 20 of 33

  1. Here we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in humans. The pipeline requires alignment files from Cell Ranger (10× Genomics...

    Authors: John K. L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Philipp Mallm, Peter Lichter and Marc Zapatka
    Citation: BMC Bioinformatics 2023 24:326
    Content type: Software Published on:

  3. Signaling systems typically involve large, structured molecules each consisting of a large number of subunits called molecule domains. In modeling such systems these domains can be considered as the main playe...

    Authors: Katrin Kolczyk, Regina Samaga, Holger Conzelmann, Sebastian Mirschel and Carsten Conradi
    Citation: BMC Bioinformatics 2012 13:251
    Content type: Research article Published on:

  4. Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP),...

    Authors: Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen Harris, Shraddha Thakkar, Guangxu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong and Hong Fang
    Citation: BMC Bioinformatics 2019 20(Suppl 2):97
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 2

  6. The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework...

    Authors: Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo and Yixue Li
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  7. Self-interacting proteins (SIPs), two or more copies of the protein that can interact with each other expressed by one gene, play a central role in the regulation of most living cells and cellular functions. A...

    Authors: Yang Li, Xue-Gang Hu, Zhu-Hong You, Li-Ping Li, Pei-Pei Li, Yan-Bin Wang and Yu-An Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 7):518
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 7

  8. The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making th...

    Authors: Terrence F Meehan, Anna Maria Masci, Amina Abdulla, Lindsay G Cowell, Judith A Blake, Christopher J Mungall and Alexander D Diehl
    Citation: BMC Bioinformatics 2011 12:6
    Content type: Methodology article Published on:

  9. The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we ...

    Authors: Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan and Tamar Schlick
    Citation: BMC Bioinformatics 2004 5:88
    Content type: Database Published on:

  10. Chronic cough affects approximately 10% of adults. The lack of ICD codes for chronic cough makes it challenging to apply supervised learning methods to predict the characteristics of chronic cough patients, th...

    Authors: Wei Shao, Xiao Luo, Zuoyi Zhang, Zhi Han, Vasu Chandrasekaran, Vladimir Turzhitsky, Vishal Bali, Anna R. Roberts, Megan Metzger, Jarod Baker, Carmen La Rosa, Jessica Weaver, Paul Dexter and Kun Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):140
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

  11. Mathematical models are nowadays widely used to describe biochemical reaction networks. One of the main reasons for this is that models facilitate the integration of a multitude of different data and data type...

    Authors: Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J Theis and Daniel Weiskopf
    Citation: BMC Bioinformatics 2013 14(Suppl 19):S2
    Content type: Research Published on:

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

  12. Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interac...

    Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo and Alfonso Urso
    Citation: BMC Bioinformatics 2020 21(Suppl 8):199
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  15. Tuberculosis (TB) represents a worldwide cause of mortality (it infects one third of the world’s population) affecting mostly developing countries, including India, and recently also developed ones due to the ...

    Authors: Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Angela Bonaccorso, Giuseppe Alessandro Parasiliti Palumbo, Epifanio Fichera, Dipendra Kumar Mitra, Kenneth B. Walker, Pere-Joan Cardona, Merce Amat, Marco Viceconti and Francesco Pappalardo
    Citation: BMC Bioinformatics 2019 20(Suppl 6):504
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  16. To reduce drug side effects and enhance their therapeutic effect compared with single drugs, drug combination research, combining two or more drugs, is highly important. Conducting in-vivo and in-vitro experim...

    Authors: Yongsun Shim, Munhwan Lee, Pil-Jong Kim and Hong-Gee Kim
    Citation: BMC Bioinformatics 2022 23:163
    Content type: Research Published on:

  17. Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance,...

    Authors: Kyle Boone, Cate Wisdom, Kyle Camarda, Paulette Spencer and Candan Tamerler
    Citation: BMC Bioinformatics 2021 22:239
    Content type: Research article Published on:

  19. This study assesses four predictive ecological models; Fuzzy Logic (FL), Recurrent Artificial Neural Network (RANN), Hybrid Evolutionary Algorithm (HEA) and multiple linear regressions (MLR) to forecast chloro...

    Authors: Sorayya Malek, Sharifah Mumtazah Syed Ahmad, Sarinder Kaur Kashmir Singh, Pozi Milow and Aishah Salleh
    Citation: BMC Bioinformatics 2011 12(Suppl 13):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 13

  20. Term identification is the task of grounding ambiguous mentions of biomedical named entities in text to unique database identifiers. Previous work on term identification has focused on studying species-specifi...

    Authors: Xinglong Wang and Michael Matthews
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  21. All proteins associate with other molecules. These associated molecules are highly predictive of the potential functions of proteins. The association of a protein and a molecule can be determined from their co...

    Authors: Kamal Taha and Paul D. Yoo
    Citation: BMC Bioinformatics 2016 17:34
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:105

  22. The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing tech...

    Authors: Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck and Michel Dumontier
    Citation: BMC Bioinformatics 2012 13:3
    Content type: Research article Published on:

  23. The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clus...

    Authors: Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether and Stefan M. Keller
    Citation: BMC Bioinformatics 2024 25:42
    Content type: Research Published on:

  24. Quantitative descriptions of amino acid similarity, expressed as probabilistic models of evolutionary interchangeability, are central to many mainstream bioinformatic procedures such as sequence alignment, hom...

    Authors: Blazej Bulka, Marie desJardins and Stephen J Freeland
    Citation: BMC Bioinformatics 2006 7:329
    Content type: Software Published on:

  25. With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising a...

    Authors: Victoria Bourgeais, Farida Zehraoui, Mohamed Ben Hamdoune and Blaise Hanczar
    Citation: BMC Bioinformatics 2021 22(Suppl 10):455
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  26. Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the t...

    Authors: Megumi Nakao, Shintaro Takemoto, Tadao Sugiura, Kazuaki Sawada, Ryosuke Kawakami, Tomomi Nemoto and Tetsuya Matsuda
    Citation: BMC Bioinformatics 2014 15:415
    Content type: Research article Published on:

  27. One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree...

    Authors: Vassily Lyubetsky, Roman Gershgorin, Alexander Seliverstov and Konstantin Gorbunov
    Citation: BMC Bioinformatics 2016 17:40
    Content type: Research article Published on:

  29. Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulat...

    Authors: Jin Ok Yang, Sohyun Hwang, Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S19
    Content type: Research Published on:

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

  33. The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data

    Authors: Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E Bourne, Julia Ponomarenko, Romulo de Castro Jr, Russell K Chan, John Sidney, Stephen S Wilson, Scott Stewart…
    Citation: BMC Bioinformatics 2006 7:341
    Content type: Database Published on:

  34. The latest works on CRISPR genome editing tools mainly employs deep learning techniques. However, deep learning models lack explainability and they are harder to reproduce. We were motivated to build an accura...

    Authors: Ali Haisam Muhammad Rafid, Md. Toufikuzzaman, Mohammad Saifur Rahman and M. Sohel Rahman
    Citation: BMC Bioinformatics 2020 21:223
    Content type: Methodology Article Published on:

  35. With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization...

    Authors: Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig and Geir Kjetil Sandve
    Citation: BMC Bioinformatics 2011 12:494
    Content type: Methodology article Published on:

  36. Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) ...

    Authors: Matthias van den Belt, Cameron Gilchrist, Thomas J. Booth, Yit-Heng Chooi, Marnix H. Medema and Mohammad Alanjary
    Citation: BMC Bioinformatics 2023 24:181
    Content type: Software Published on:

  37. In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare...

    Authors: Jiajie Peng, Yadong Wang and Jin Chen
    Citation: BMC Bioinformatics 2014 15(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 2

  40. Clustering is a widely used collection of unsupervised learning techniques for identifying natural classes within a data set. It is often used in bioinformatics to infer population substructure. Genomic data a...

    Authors: Bertrand S. Clarke, Saeid Amiri and Jennifer L. Clarke
    Citation: BMC Bioinformatics 2016 17:380
    Content type: Software Published on:

  41. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships betw...

    Authors: Yubin Xiao, Zheng Xiao, Xiang Feng, Zhiping Chen, Linai Kuang and Lei Wang
    Citation: BMC Bioinformatics 2020 21:555
    Content type: Methodology article Published on:

  42. Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwo...

    Authors: Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J Smit, Michel A Westenberg and Gunnar W Klau
    Citation: BMC Bioinformatics 2014 15:201
    Content type: Research article Published on:

  43. Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome ...

    Authors: Julie M Allen, Daisie I Huang, Quentin C Cronk and Kevin P Johnson
    Citation: BMC Bioinformatics 2015 16:98
    Content type: Software Published on:

  44. Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e....

    Authors: Peter Bajcsy, Soweon Yoon, Stephen J. Florczyk, Nathan A. Hotaling, Mylene Simon, Piotr M. Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr, Mary Brady and Ram D. Sriram
    Citation: BMC Bioinformatics 2017 18:526
    Content type: Research Article Published on:

  45. Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations betwee...

    Authors: Lina Ma, Sitao Zhang, Qi Liang, Wenting Huang, Hui Wang, Emily Pan, Ping Xu, Shuguang Zhang, Fei Tao, Jin Tang and Rui Qing
    Citation: BMC Bioinformatics 2023 24:360
    Content type: Research Published on:

  46. The breakthrough high-throughput measurement of the cis-regulatory activity of millions of randomly generated promoters provides an unprecedented opportunity to systematically decode the cis-regulatory logic t...

    Authors: Il-Youp Kwak, Byeong-Chan Kim, Juhyun Lee, Taein Kang, Daniel J. Garry, Jianyi Zhang and Wuming Gong
    Citation: BMC Bioinformatics 2024 25:81
    Content type: Research Published on:

  47. The amount of biomedical literature available is growing at an explosive speed, but a large amount of useful information remains undiscovered in it. Researchers can make informed biomedical hypotheses through ...

    Authors: Liangxi Cheng, Hongfei Lin, Feng Zhou, Zhihao Yang and Jian Wang
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  48. The response of many biomedical systems can be modelled using a linear combination of damped exponential functions. The approximation parameters, based on equally spaced samples, can be obtained using Prony’s ...

    Authors: A. Fernández Rodríguez, L. de Santiago Rodrigo, E. López Guillén, J. M. Rodríguez Ascariz, J. M. Miguel Jiménez and Luciano Boquete
    Citation: BMC Bioinformatics 2018 19:451
    Content type: Software Published on:

  49. The position of a sentence in a document has been traditionally considered an indicator of the relevance of the sentence, and therefore it is frequently used by automatic summarization systems as an attribute ...

    Authors: Laura Plaza and Jorge Carrillo-de-Albornoz
    Citation: BMC Bioinformatics 2013 14:71
    Content type: Research article Published on:

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