Skip to main content

Articles

Page 93 of 249

  1. Variations in DNA copy number have an important contribution to the development of several diseases, including autism, schizophrenia and cancer. Single-cell sequencing technology allows the dissection of genom...

    Authors: Changsheng Zhang, Hongmin Cai, Jingying Huang and Yan Song
    Citation: BMC Bioinformatics 2016 17:384
    Content type: Research Article Published on:

  2. 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:

  3. Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and ...

    Authors: Wenling E. Chang, Matthew W. Peterson, Christopher D. Garay and Tonia Korves
    Citation: BMC Bioinformatics 2016 17:379
    Content type: Software Published on:

  4. “Tail-anchored (TA) proteins” is a collective term for transmembrane proteins with a C-terminal transmembrane domain (TMD) and without an N-terminal signal sequence. TA proteins account for approximately 3–5 %...

    Authors: Shunsuke Shigemitsu, Wei Cao, Tohru Terada and Kentaro Shimizu
    Citation: BMC Bioinformatics 2016 17:378
    Content type: Research Article Published on:

  5. Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-se...

    Authors: Lydia Müller, Daniel Gerighausen, Mariam Farman and Dirk Zeckzer
    Citation: BMC Bioinformatics 2016 17:377
    Content type: Methodology Article Published on:

  6. Soma localization is an important step in computational neuroscience to map neuronal circuits. However, locating somas from large-scale and complicated datasets is challenging. The challenges primarily origina...

    Authors: Shenghua Cheng, Tingwei Quan, Xiaomao Liu and Shaoqun Zeng
    Citation: BMC Bioinformatics 2016 17:375
    Content type: Methodology article Published on:

  7. Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerge...

    Authors: Jose M González-Calabozo, Francisco J Valverde-Albacete and Carmen Peláez-Moreno
    Citation: BMC Bioinformatics 2016 17:374
    Content type: Methodology Article Published on:

  8. Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the ...

    Authors: Ricardo Cerri, Rodrigo C. Barros, André C. P. L. F. de Carvalho and Yaochu Jin
    Citation: BMC Bioinformatics 2016 17:373
    Content type: Methodology Article Published on:

  9. Protein complexes are the key molecular entities to perform many essential biological functions. In recent years, high-throughput experimental techniques have generated a large amount of protein interaction da...

    Authors: Le Ou-Yang, Xiao-Fei Zhang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu, Zhiyong Liu and Hong Yan
    Citation: BMC Bioinformatics 2016 17:371
    Content type: Research Article Published on:

  12. Over the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these dataset...

    Authors: David Angeles-Albores, Raymond Y. N. Lee, Juancarlos Chan and Paul W. Sternberg
    Citation: BMC Bioinformatics 2016 17:366
    Content type: Methodology Article Published on:

  14. Allele specific expression (ASE) has become an important phenotype, being utilized for the detection of cis-regulatory variation, nonsense mediated decay and imprinting in the personal genome, and has been used t...

    Authors: Alan Hodgkinson, Jean-Christophe Grenier, Elias Gbeha and Philip Awadalla
    Citation: BMC Bioinformatics 2016 17:364
    Content type: Methodology article Published on:

  15. Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality redu...

    Authors: David A. duVerle, Sohiya Yotsukura, Seitaro Nomura, Hiroyuki Aburatani and Koji Tsuda
    Citation: BMC Bioinformatics 2016 17:363
    Content type: Software Published on:

  16. Protein secondary structure prediction (SSP) has been an area of intense research interest. Despite advances in recent methods conducted on large datasets, the estimated upper limit accuracy is yet to be reach...

    Authors: Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram and Andrzej Kolinski
    Citation: BMC Bioinformatics 2016 17:362
    Content type: Methodology Article Published on:

  17. The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical comp...

    Authors: Zhuoyi Huang, Navin Rustagi, Narayanan Veeraraghavan, Andrew Carroll, Richard Gibbs, Eric Boerwinkle, Manjunath Gorentla Venkata and Fuli Yu
    Citation: BMC Bioinformatics 2016 17:361
    Content type: Methodology article Published on:

  19. Several recent studies have used the Minimum Dominating Set (MDS) model to identify driver nodes, which provide the control of the underlying networks, in protein interaction networks. There may exist multiple...

    Authors: Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu and Hong Yan
    Citation: BMC Bioinformatics 2016 17:358
    Content type: Research Article Published on:

  20. Rapid technological innovation for the generation of single-cell genomics data presents new challenges and opportunities for bioinformatics analysis. One such area lies in the development of new ways to train ...

    Authors: Chee Yee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher and Berthold Göttgens
    Citation: BMC Bioinformatics 2016 17:355
    Content type: Methodology article Published on:

  21. Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the...

    Authors: Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vitor Vasconcelos and Agostinho Antunes
    Citation: BMC Bioinformatics 2016 17:354
    Content type: Software Published on:

  23. Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for ne...

    Authors: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
    Citation: BMC Bioinformatics 2016 17:352
    Content type: Methodology Article Published on:

  24. It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit this information when the number of determinan...

    Authors: Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe and Arnoldo Frigessi
    Citation: BMC Bioinformatics 2016 17:344
    Content type: Methodology Article Published on:

  25. The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA—the backbone of microbiome analyses—allows ...

    Authors: Helena Mendes-Soares, Michael Mundy, Luis Mendes Soares and Nicholas Chia
    Citation: BMC Bioinformatics 2016 17:343
    Content type: Software Published on:

  26. Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most benign, they reduce the power of statistical tes...

    Authors: Yalchin Oytam, Fariborz Sobhanmanesh, Konsta Duesing, Joshua C. Bowden, Megan Osmond-McLeod and Jason Ross
    Citation: BMC Bioinformatics 2016 17:332
    Content type: Methodology article Published on:

  27. The Random Forest (RF) algorithm for supervised machine learning is an ensemble learning method widely used in science and many other fields. Its popularity has been increasing, but relatively few studies addr...

    Authors: Barbara F.F. Huang and Paul C. Boutros
    Citation: BMC Bioinformatics 2016 17:331
    Content type: Methodology article Published on:

  28. Metaheuristics are widely used to solve large combinatorial optimization problems in bioinformatics because of the huge set of possible solutions. Two representative problems are gene selection for cancer clas...

    Authors: Juan A. Gomez-Pulido, Jose L. Cerrada-Barrios, Sebastian Trinidad-Amado, Jose M. Lanza-Gutierrez, Ramon A. Fernandez-Diaz, Broderick Crawford and Ricardo Soto
    Citation: BMC Bioinformatics 2016 17:330
    Content type: Research Article Published on:

  30. This paper describes a new MSA tool called PnpProbs, which constructs better multiple sequence alignments by better handling of guide trees. It classifies sequences into two types: normally related and distant...

    Authors: Yongtao Ye, Tak-Wah Lam and Hing-Fung Ting
    Citation: BMC Bioinformatics 2016 17(Suppl 8):285
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  31. Non-Negative Matrix factorization has become an essential tool for feature extraction in a wide spectrum of applications. In the present work, our objective is to extend the applicability of the method to the ...

    Authors: Stéphane Chrétien, Christophe Guyeux, Bastien Conesa, Régis Delage-Mouroux, Michèle Jouvenot, Philippe Huetz and Françoise Descôtes
    Citation: BMC Bioinformatics 2016 17(Suppl 8):284
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  32. Metagenomics is a cultivation-independent approach that enables the study of the genomic composition of microbes present in an environment. Metagenomic samples are routinely sequenced using next-generation seq...

    Authors: Cuncong Zhong, Youngik Yang and Shibu Yooseph
    Citation: BMC Bioinformatics 2016 17(Suppl 8):283
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  33. There has been paid more and more attention to supervised classification models in the area of predicting drug-target interactions (DTIs). However, in terms of classification, unavoidable missing DTIs in data ...

    Authors: Jian-Yu Shi, Jia-Xin Li and Hui-Meng Lu
    Citation: BMC Bioinformatics 2016 17(Suppl 8):282
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  34. The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biolog...

    Authors: Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang and Yaohang Li
    Citation: BMC Bioinformatics 2016 17(Suppl 8):281
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  35. Herein, the predicted atomic structures of five representative sequence variants of the reverse transcriptase protein (RT) of hepatitis B virus (HBV), sampled from patients with rapid or slow response to tenof...

    Authors: Xiaojun Xu, Hong Thai, Kathryn M. Kitrinos, Guoliang Xia, Anuj Gaggar, Matthew Paulson, Lilia Ganova-Raeva, Yury Khudyakov and James Lara
    Citation: BMC Bioinformatics 2016 17(Suppl 8):280
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  36. Essential proteins play an indispensable role in the cellular survival and development. There have been a series of biological experimental methods for finding essential proteins; however they are time-consumi...

    Authors: Gaoshi Li, Min Li, Jianxin Wang, Jingli Wu, Fang-Xiang Wu and Yi Pan
    Citation: BMC Bioinformatics 2016 17(Suppl 8):279
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  37. HIV/AIDS is a serious threat to public health. The emergence of drug resistance mutations diminishes the effectiveness of drug therapy for HIV/AIDS. Developing a computational prediction of drug resistance phe...

    Authors: ChenHsiang Shen, Xiaxia Yu, Robert W. Harrison and Irene T. Weber
    Citation: BMC Bioinformatics 2016 17(Suppl 8):278
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  38. Comparative genomics can leverage the vast amount of available genomic sequences to reconstruct and analyze transcriptional regulatory networks in Bacteria, but the efficacy of this approach hinges on the abil...

    Authors: Sefa Kılıç and Ivan Erill
    Citation: BMC Bioinformatics 2016 17(Suppl 8):277
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  39. Microbial genomes at the National Center for Biotechnology Information (NCBI) represent a large collection of more than 35,000 assemblies. There are several complexities associated with the data: a great varia...

    Authors: Leonid Zaslavsky, Stacy Ciufo, Boris Fedorov and Tatiana Tatusova
    Citation: BMC Bioinformatics 2016 17(Suppl 8):276
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 8

  40. Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, and also for discriminating between uni...

    Authors: Sumudu P. Leelananda, Andrzej Kloczkowski and Robert L. Jernigan
    Citation: BMC Bioinformatics 2016 17:328
    Content type: Research article Published on:

  41. High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be ...

    Authors: Stefanie Hieke, Axel Benner, Richard F. Schlenl, Martin Schumacher, Lars Bullinger and Harald Binder
    Citation: BMC Bioinformatics 2016 17:327
    Content type: Research Article Published on:

  44. Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available method...

    Authors: Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong and Ping Ma
    Citation: BMC Bioinformatics 2016 17:324
    Content type: Methodology Article Published on:

  46. Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, an...

    Authors: Xue Zhang, Wangxin Xiao, Marcio Luis Acencio, Ney Lemke and Xujing Wang
    Citation: BMC Bioinformatics 2016 17:322
    Content type: Methodology article Published on:

  47. Biological/genetic data is a complex mix of various forms or topologies which makes it quite difficult to analyze. An abundance of such data in this modern era requires the development of sophisticated statist...

    Authors: Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo and Tatsuhiko Tsunoda
    Citation: BMC Bioinformatics 2016 17:319
    Content type: Research article Published on:

  48. Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks...

    Authors: Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek and Kourosh Zarringhalam
    Citation: BMC Bioinformatics 2016 17:318
    Content type: Research Article Published on:

  50. Reactive oxygen species can modify the structure and function of proteins and may also act as important signaling molecules in various cellular processes. Cysteine thiol groups of proteins are particularly sus...

    Authors: Ming-an Sun, Qing Zhang, Yejun Wang, Wei Ge and Dianjing Guo
    Citation: BMC Bioinformatics 2016 17:316
    Content type: Methodology article Published on:

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