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  1. 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

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  2. 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

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  3. 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

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  4. 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

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  6. 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

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  7. 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

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  9. 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

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  10. 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

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  11. 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

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  13. 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

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  14. 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

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  16. 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

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  17. 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

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  18. 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

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  20. 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

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  21. 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

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  23. 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

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  25. 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

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  26. 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

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  27. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  36. 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

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  39. Currently the combination of molecular tools, imaging techniques and analysis software offer the possibility of studying gene activity through the use of fluorescent reporters and infer its distribution within...

    Authors: David R. Espeso, Elena Algar, Esteban Martínez-García and Víctor de Lorenzo

    Citation: BMC Bioinformatics 2020 21:224

    Content type: Methodology article

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  40. 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

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  43. The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly incre...

    Authors: William S. Pearman, Nikki E. Freed and Olin K. Silander

    Citation: BMC Bioinformatics 2020 21:220

    Content type: Research article

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  44. Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among t...

    Authors: Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva and Riccardo Bellazzi

    Citation: BMC Bioinformatics 2020 21:219

    Content type: Methodology article

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  45. Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th...

    Authors: Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman

    Citation: BMC Bioinformatics 2020 21:217

    Content type: Research article

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  46. The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a m...

    Authors: Kitsuchart Pasupa, Wanthanee Rathasamuth and Sissades Tongsima

    Citation: BMC Bioinformatics 2020 21:216

    Content type: Methodology Article

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  47. Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell o...

    Authors: Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He and Patrick Flaherty

    Citation: BMC Bioinformatics 2020 21:215

    Content type: Software

    Published on:

  48. Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription ...

    Authors: Samuel J. Roth, Sven Heinz and Christopher Benner

    Citation: BMC Bioinformatics 2020 21:214

    Content type: Software

    Published on:

  50. Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification,...

    Authors: Azree Nazri, Olalekan Agbolade, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah

    Citation: BMC Bioinformatics 2020 21:208

    Content type: Research article

    Published on:

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