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  1. The evolution of next-generation sequencing (NGS) technologies has led to increased focus on RNA-Seq. Many bioinformatic tools have been developed for RNA-Seq analysis, each with unique performance characteris...

    Authors: Jérôme Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes and Nicolas Philippe
    Citation: BMC Bioinformatics 2017 18:428
    Content type: Software Published on:

  2. Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has ...

    Authors: Duo Xu, Yousef Jaber, Pavlos Pavlidis and Omer Gokcumen
    Citation: BMC Bioinformatics 2017 18:426
    Content type: Software Published on:

  3. Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have b...

    Authors: Ying Wang, Kun Wang, Yang Young Lu and Fengzhu Sun
    Citation: BMC Bioinformatics 2017 18:425
    Content type: Methodology Article Published on:

  4. The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the u...

    Authors: José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau and Joaquín Dopazo
    Citation: BMC Bioinformatics 2017 18:421
    Content type: Software Published on:

  5. Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012,...

    Authors: Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu and Jianlin Cheng
    Citation: BMC Bioinformatics 2017 18:417
    Content type: Methodology Article Published on:

  7. The ability to efficiently search and filter datasets depends on access to high quality metadata. While most biomedical repositories require data submitters to provide a minimal set of metadata, some such as t...

    Authors: Wei Hu, Amrapali Zaveri, Honglei Qiu and Michel Dumontier
    Citation: BMC Bioinformatics 2017 18:415
    Content type: Methodology Article Published on:

  8. Aging is characterized by a gradual breakdown of cellular structures. Nuclear abnormality is a hallmark of progeria in human. Analysis of age-dependent nuclear morphological changes in Caenorhabditis elegans is o...

    Authors: Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-Mei Li, Meng-Qiu Dong, Heng Mao and Louis Tao
    Citation: BMC Bioinformatics 2017 18:412
    Content type: Research Article Published on:

  9. RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previou...

    Authors: Matthias Zytnicki
    Citation: BMC Bioinformatics 2017 18:411
    Content type: Software Published on:

  10. A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease associatio...

    Authors: Alexandre V. Fassio, Pedro M. Martins, Samuel da S. Guimarães, Sócrates S. A. Junior, Vagner S. Ribeiro, Raquel C. de Melo-Minardi and Sabrina de A. Silveira
    Citation: BMC Bioinformatics 2017 18(Suppl 10):403
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  11. We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons...

    Authors: Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram and Felix Schürmann
    Citation: BMC Bioinformatics 2017 18(Suppl 10):402
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  12. The advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organi...

    Authors: Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P. Telles, Gabriela Vaz Meirelles and Rosane Minghim
    Citation: BMC Bioinformatics 2017 18(Suppl 10):395
    Content type: Software Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  13. Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as micr...

    Authors: Lan Huong Nguyen and Susan Holmes
    Citation: BMC Bioinformatics 2017 18(Suppl 10):394
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  14. Dispersed biomedical databases limit user exploration to generate structured knowledge. Linked Data unifies data structures and makes the dispersed data easy to search across resources, but it lacks supporting hu...

    Authors: Chen He, Luana Micallef, Zia-ur-Rehman Tanoli, Samuel Kaski, Tero Aittokallio and Giulio Jacucci
    Citation: BMC Bioinformatics 2017 18(Suppl 10):393
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  15. Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of n...

    Authors: Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan and Rakesh K Mishra
    Citation: BMC Bioinformatics 2017 18(Suppl 10):392
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 10

  16. With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method th...

    Authors: Michael Kern, Alexander Lex, Nils Gehlenborg and Chris R. Johnson
    Citation: BMC Bioinformatics 2017 18:406
    Content type: Software Published on:

  17. Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and pro...

    Authors: Jared Ostmeyer, Scott Christley, William H. Rounds, Inimary Toby, Benjamin M. Greenberg, Nancy L. Monson and Lindsay G. Cowell
    Citation: BMC Bioinformatics 2017 18:401
    Content type: Research Article Published on:

  18. Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only ...

    Authors: Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans and Jo Vandesompele
    Citation: BMC Bioinformatics 2017 18:400
    Content type: Software Published on:

  19. A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological p...

    Authors: Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos and Theodore Dalamagas
    Citation: BMC Bioinformatics 2017 18:399
    Content type: Software Published on:

  21. Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codo...

    Authors: John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan and Chava Kimchi-Sarfaty
    Citation: BMC Bioinformatics 2017 18:391
    Content type: Database Published on:

  24. Colorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through t...

    Authors: Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun and Qingling Zhang
    Citation: BMC Bioinformatics 2017 18:388
    Content type: Research Article Published on:

  25. As a newly emerged research area, RNA epigenetics has drawn increasing attention recently for the participation of RNA methylation and other modifications in a number of crucial biological processes. Thanks to...

    Authors: Lian Liu, Shao-Wu Zhang, Yufei Huang and Jia Meng
    Citation: BMC Bioinformatics 2017 18:387
    Content type: Methodology Article Published on:

  26. Residue-residue contacts are key features for accurate de novo protein structure prediction. For the optimal utilization of these predicted contacts in folding proteins accurately, it is important to study the...

    Authors: Badri Adhikari and Jianlin Cheng
    Citation: BMC Bioinformatics 2017 18:380
    Content type: Research Article Published on:

  27. Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the re...

    Authors: Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He and Hongpeng Wang
    Citation: BMC Bioinformatics 2017 18:379
    Content type: Research Article Published on:

  28. Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done bef...

    Authors: Saghi Nojoomi and Patrice Koehl
    Citation: BMC Bioinformatics 2017 18:378
    Content type: Methodology Article Published on:

  29. A multivariate genome-wide association test is proposed for analyzing data on multivariate quantitative phenotypes collected from related subjects. The proposed method is a two-step approach. The first step mo...

    Authors: James J. Yang, L Keoki Williams and Anne Buu
    Citation: BMC Bioinformatics 2017 18:376
    Content type: Methodology Article Published on:

  30. Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent bu...

    Authors: Xin-Ping Xie, Yu-Feng Xie and Hong-Qiang Wang
    Citation: BMC Bioinformatics 2017 18:375
    Content type: Research Article Published on:

  31. Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced err...

    Authors: Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer and Jan Fostier
    Citation: BMC Bioinformatics 2017 18:374
    Content type: Research Article Published on:

  33. Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...

    Authors: K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer and Lawrence E. Hunter
    Citation: BMC Bioinformatics 2017 18:372
    Content type: Research Article Published on:

  34. Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...

    Authors: Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider
    Citation: BMC Bioinformatics 2017 18:371
    Content type: Software Published on:

  35. Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of ...

    Authors: Seirana Hashemi, Abbas Nowzari Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam and Zahra Razaghi-Moghadam
    Citation: BMC Bioinformatics 2017 18:370
    Content type: Research Article Published on:

  36. Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...

    Authors: Olivier Sheik Amamuddy, Nigel T. Bishop and Özlem Tastan Bishop
    Citation: BMC Bioinformatics 2017 18:369
    Content type: Research Article Published on:

  38. Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotate...

    Authors: Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin and Nevin D. Young
    Citation: BMC Bioinformatics 2017 18:367
    Content type: Software Published on:

  39. As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasing...

    Authors: Lisa Katharina Blaß, Christian Weyler and Elmar Heinzle
    Citation: BMC Bioinformatics 2017 18:366
    Content type: Research Article Published on:

  40. Traction Force Microscopy (TFM) is a widespread technique to estimate the tractions that cells exert on the surrounding substrate. To recover the tractions, it is necessary to solve an inverse problem, which i...

    Authors: Alejandro Suñé-Auñón, Alvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck and Arrate Muñoz-Barrutia
    Citation: BMC Bioinformatics 2017 18:365
    Content type: Research Article Published on:

  42. Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS...

    Authors: Carlos Guzman and Iván D’Orso
    Citation: BMC Bioinformatics 2017 18:363
    Content type: Software Published on:

  43. Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...

    Authors: Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson and Matthew W. Vaughn
    Citation: BMC Bioinformatics 2017 18:362
    Content type: Software Published on:

  44. Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is imp...

    Authors: Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram and John Pestian
    Citation: BMC Bioinformatics 2017 18:361
    Content type: Methodology Article Published on:

  45. Histopathology images are critical for medical diagnosis, e.g., cancer and its treatment. A standard histopathology slice can be easily scanned at a high resolution of, say, 200,000×200,000 pixels. These high ...

    Authors: Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai and Eric I-Chao Chang
    Citation: BMC Bioinformatics 2017 18:360
    Content type: Research Article Published on:

  46. MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biologica...

    Authors: Daniel Amsel, Andreas Vilcinskas and André Billion
    Citation: BMC Bioinformatics 2017 18:359
    Content type: Research Article Published on:

  47. Disease progression models are important for understanding the critical steps during the development of diseases. The models are imbedded in a statistical framework to deal with random variations due to biolog...

    Authors: Katrin Hainke, Sebastian Szugat, Roland Fried and Jörg Rahnenführer
    Citation: BMC Bioinformatics 2017 18:358
    Content type: Research Article Published on:

  50. Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in vario...

    Authors: Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw and Jiang Qian
    Citation: BMC Bioinformatics 2017 18:355
    Content type: Research Article Published on:

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