Skip to main content

Articles

Page 46 of 249

  1. Even though we have established a few risk factors for metastatic breast cancer (MBC) through epidemiologic studies, these risk factors have not proven to be effective in predicting an individual’s risk of develo...

    Authors: Xia Jiang, Alan Wells, Adam Brufsky, Darshan Shetty, Kahmil Shajihan and Richard E. Neapolitan
    Citation: BMC Bioinformatics 2020 21:298
    Content type: Methodology article Published on:

  3. The human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing, the golden standard technology f...

    Authors: Yong Zhang, Yongsheng Chen, Huixin Xu, Junbin Fang, Zijian Zhao, Weipeng Hu, Xiaoqin Yang, Jia Ye, Yun Cheng, Jiayin Wang, Weiqiang Sun, Jian Wang, Huanming Yang, Jing Yan and Lin Fang
    Citation: BMC Bioinformatics 2020 21:295
    Content type: Software Published on:

  4. Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Neverthele...

    Authors: Javier Calvelo, Hernán Juan, Héctor Musto, Uriel Koziol and Andrés Iriarte
    Citation: BMC Bioinformatics 2020 21:293
    Content type: Software Published on:

  7. New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring t...

    Authors: Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich and Andreas Dräger
    Citation: BMC Bioinformatics 2020 21:130
    Content type: Methodology Article Published on:

  8. The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contri...

    Authors: Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong and Julie C. Mitchell
    Citation: BMC Bioinformatics 2020 21:289
    Content type: Research article Published on:

  9. Cancer is a highly heterogeneous disease with varying responses to anti-cancer drugs. Although several attempts have been made to predict the anti-cancer therapeutic responses, there remains a great need to de...

    Authors: Youngchul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal and Minjung Kim
    Citation: BMC Bioinformatics 2020 21:288
    Content type: Methodology article Published on:

  10. Software tools for analyzing DNA methylation do not provide graphical results which can be easily identified, but huge text files containing the alignment of the samples and their methylation status at a resol...

    Authors: Lisardo Fernández, Mariano Pérez, Ricardo Olanda, Juan M. Orduña and Joan Marquez-Molins
    Citation: BMC Bioinformatics 2020 21:287
    Content type: Software Published on:

  12. The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thu...

    Authors: Miika Leinonen and Leena Salmela
    Citation: BMC Bioinformatics 2020 21:285
    Content type: Methodology article Published on:

  13. 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:

  14. Diabetic retinopathy (DR), the most common cause of vision loss, is caused by damage to the small blood vessels in the retina. If untreated, it may result in varying degrees of vision loss and even blindness. ...

    Authors: Mahmut Karakaya and Recep E. Hacisoftaoglu
    Citation: BMC Bioinformatics 2020 21(Suppl 4):259
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 4

  16. A key use of high throughput sequencing technology is the sequencing and assembly of full genome sequences. These genome assemblies are commonly assessed using statistics relating to contiguity of the assembly...

    Authors: Adam Thrash, Federico Hoffmann and Andy Perkins
    Citation: BMC Bioinformatics 2020 21(Suppl 4):249
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 4

  17. Identifying drug-target interaction is a key element in drug discovery. In silico prediction of drug-target interaction can speed up the process of identifying unknown interactions between drugs and target pro...

    Authors: Hafez Eslami Manoochehri and Mehrdad Nourani
    Citation: BMC Bioinformatics 2020 21(Suppl 4):248
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 4

  18. Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the...

    Authors: Yongsheng Bai, Steve Baker, Kevin Exoo, Xingqin Dai, Lizhong Ding, Naureen Aslam Khattak, Hongtao Li, Hannah Liu and Xiaoming Liu
    Citation: BMC Bioinformatics 2020 21(Suppl 4):247
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 4

  19. Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based me...

    Authors: Tong Liu and Zheng Wang
    Citation: BMC Bioinformatics 2020 21(Suppl 4):246
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 4

  20. The problem of assessing associations between multiple omics data including genomics and metabolomics data to identify biomarkers potentially predictive of complex diseases has garnered considerable research i...

    Authors: Haileab Hilafu, Sandra E. Safo and Lillian Haine
    Citation: BMC Bioinformatics 2020 21:283
    Content type: Methodology article Published on:

  21. During transcription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to control the gene expression. Alterations in groups of TF-binding profiles (i.e. “co-binding changes”...

    Authors: Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy and Mark Gerstein
    Citation: BMC Bioinformatics 2020 21:281
    Content type: Methodology article Published on:

  22. Image-based high throughput (HT) screening provides a rich source of information on dynamic cellular response to external perturbations. The large quantity of data generated necessitates computer-aided quality...

    Authors: Minhua Qiu, Bin Zhou, Frederick Lo, Steven Cook, Jason Chyba, Doug Quackenbush, Jason Matzen, Zhizhong Li, Puiying Annie Mak, Kaisheng Chen and Yingyao Zhou
    Citation: BMC Bioinformatics 2020 21:280
    Content type: Methodology article Published on:

  23. Immunotherapy is a promising route towards personalized cancer treatment. A key algorithmic challenge in this process is to decide if a given peptide (neoepitope) binds with the major histocompatibility comple...

    Authors: Johanna Vielhaben, Markus Wenzel, Wojciech Samek and Nils Strodthoff
    Citation: BMC Bioinformatics 2020 21:279
    Content type: Software Published on:

  25. The standard lasso penalty and its extensions are commonly used to develop a regularized regression model while selecting candidate predictor variables on a time-to-event outcome in high-dimensional data. Howe...

    Authors: Shaima Belhechmi, Riccardo De Bin, Federico Rotolo and Stefan Michiels
    Citation: BMC Bioinformatics 2020 21:277
    Content type: Methodology article Published on:

  26. Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutat...

    Authors: José Renato M. S. Barroso, Diego Mariano, Sandro R. Dias, Rafael E. O. Rocha, Lucianna H. Santos, Ronaldo A. P. Nagem and Raquel C. de Melo-Minardi
    Citation: BMC Bioinformatics 2020 21:275
    Content type: Software Published on:

  28. Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variatio...

    Authors: Måns Magnusson, Jesper Eisfeldt, Daniel Nilsson, Adam Rosenbaum, Valtteri Wirta, Anna Lindstrand, Anna Wedell and Henrik Stranneheim
    Citation: BMC Bioinformatics 2020 21:273
    Content type: Software Published on:

  29. Chromatin 3D conformation plays important roles in regulating gene or protein functions. High-throughout chromosome conformation capture (3C)-based technologies, such as Hi-C, have been exploited to acquire th...

    Authors: Fang-Zhen Li, Zhi-E Liu, Xiu-Yuan Li, Li-Mei Bu, Hong-Xia Bu, Hui Liu and Cai-Ming Zhang
    Citation: BMC Bioinformatics 2020 21:272
    Content type: Methodology Published on:

  30. Systematic technical effects—also called batch effects—are a considerable challenge when analyzing DNA methylation (DNAm) microarray data, because they can lead to false results when confounded with the variab...

    Authors: Tristan Zindler, Helge Frieling, Alexandra Neyazi, Stefan Bleich and Eva Friedel
    Citation: BMC Bioinformatics 2020 21:271
    Content type: Research article Published on:

  32. High-throughput technologies enable the cost-effective collection and analysis of DNA methylation data throughout the human genome. This naturally entails missing values management that can complicate the anal...

    Authors: Pietro Di Lena, Claudia Sala, Andrea Prodi and Christine Nardini
    Citation: BMC Bioinformatics 2020 21:268
    Content type: Research article Published on:

  33. As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis an...

    Authors: Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan and Kristin C. Gunsalus
    Citation: BMC Bioinformatics 2020 21:267
    Content type: Software Published on:

  35. The combination of systematic evolution of ligands by exponential enrichment (SELEX) and deep sequencing is termed high-throughput (HT)-SELEX, which enables searching aptamer candidates from a massive amount o...

    Authors: Shintaro Kato, Takayoshi Ono, Hirotaka Minagawa, Katsunori Horii, Ikuo Shiratori, Iwao Waga, Koichi Ito and Takafumi Aoki
    Citation: BMC Bioinformatics 2020 21:263
    Content type: Methodology article Published on:

  36. Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene cat...

    Authors: Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski and Lee Ann McCue
    Citation: BMC Bioinformatics 2020 21:257
    Content type: Software Published on:

  37. In 2009, a novel influenza vaccine was distributed worldwide to combat the H1N1 influenza “swine flu” pandemic. However, antibodies induced by the vaccine display differences in their specificity and cross-rea...

    Authors: Christopher S. Anderson, Mark Y. Sangster, Hongmei Yang, Thomas J. Mariani, Sidhartha Chaudhury and David J. Topham
    Citation: BMC Bioinformatics 2020 21:256
    Content type: Research article Published on:

  39. Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermo...

    Authors: Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang and Zhen-Xia Chen
    Citation: BMC Bioinformatics 2020 21:252
    Content type: Software Published on:

  40. Models including an interaction term and performing a joint test of SNP and/or interaction effect are often used to discover Gene-Environment (GxE) interactions. When the environmental exposure is a binary var...

    Authors: Vincent Laville, Timothy Majarian, Paul S. de Vries, Amy R. Bentley, Mary F. Feitosa, Yun J. Sung, D. C. Rao, Alisa Manning and Hugues Aschard
    Citation: BMC Bioinformatics 2020 21:251
    Content type: Software Published on:

  42. Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole b...

    Authors: Raúl Aguirre-Gamboa, Niek de Klein, Jennifer di Tommaso, Annique Claringbould, Monique GP van der Wijst, Dylan de Vries, Harm Brugge, Roy Oelen, Urmo Võsa, Maria M. Zorro, Xiaojin Chu, Olivier B. Bakker, Zuzanna Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu…
    Citation: BMC Bioinformatics 2020 21:243
    Content type: Methodology article Published on:

  44. Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Car...

    Authors: Mihály Koltai, Vincent Noel, Andrei Zinovyev, Laurence Calzone and Emmanuel Barillot
    Citation: BMC Bioinformatics 2020 21:241
    Content type: Methodology Article Published on:

  45. Single-cell RNA sequencing (scRNA-seq) provides an effective tool to investigate the transcriptomic characteristics at the single-cell resolution. Due to the low amounts of transcripts in single cells and the ...

    Authors: Yang Qi, Yang Guo, Huixin Jiao and Xuequn Shang
    Citation: BMC Bioinformatics 2020 21:240
    Content type: Methodology Article Published on:

  46. Phytochemicals and other molecules in foods elicit positive health benefits, often by poorly established or unknown mechanisms. While there is a wealth of data on the biological and biophysical properties of d...

    Authors: Kenneth E. Westerman, Sean Harrington, Jose M. Ordovas and Laurence D. Parnell
    Citation: BMC Bioinformatics 2020 21:238
    Content type: Software Published on:

  48. The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is nece...

    Authors: Jianwei Li, Xiaoyu Ma, Xichuan Li and Junhua Gu
    Citation: BMC Bioinformatics 2020 21:236
    Content type: Methodology article Published on:

  49. The number of applications of deep learning algorithms in bioinformatics is increasing as they usually achieve superior performance over classical approaches, especially, when bigger training datasets are avai...

    Authors: Hesham ElAbd, Yana Bromberg, Adrienne Hoarfrost, Tobias Lenz, Andre Franke and Mareike Wendorff
    Citation: BMC Bioinformatics 2020 21:235
    Content type: Methodology article Published on:

  50. The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing...

    Authors: Alexis Robitaille, Rosario N. Brancaccio, Sankhadeep Dutta, Dana E. Rollison, Marcis Leja, Nicole Fischer, Adam Grundhoff, Tarik Gheit, Massimo Tommasino and Magali Olivier
    Citation: BMC Bioinformatics 2020 21:233
    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