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  1. 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:

  2. 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

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  3. 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:

  4. 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:

  5. 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

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  6. 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:

  7. 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

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  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma and accounts for cancer-related deaths. Survival rates are very low when the tumor is discovered in the late-stage. Th...

    Authors: Fangjun Li, Mu Yang, Yunhe Li, Mingqiang Zhang, Wenjuan Wang, Dongfeng Yuan and Dongqi Tang

    Citation: BMC Bioinformatics 2020 21:232

    Content type: Research article

    Published on:

  37. During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research field. While numerous existing methods focus on the in...

    Authors: Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt and Martin Hofmann-Apitius

    Citation: BMC Bioinformatics 2020 21:231

    Content type: Methodology article

    Published on:

  38. Inferring diseases related to the patient’s electronic medical records (EMRs) is of great significance for assisting doctor diagnosis. Several recent prediction methods have shown that deep learning-based meth...

    Authors: Tong Wang, Ping Xuan, Zonglin Liu and Tiangang Zhang

    Citation: BMC Bioinformatics 2020 21:230

    Content type: Methodology article

    Published on:

  39. Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all ...

    Authors: William Meyerson, John Leisman, Fabio C. P. Navarro and Mark Gerstein

    Citation: BMC Bioinformatics 2020 21:227

    Content type: Research article

    Published on:

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