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  1. Drugs achieve pharmacological functions by acting on target proteins. Identifying interactions between drugs and target proteins is an essential task in old drug repositioning and new drug discovery. To recomm...

    Authors: Chunyan Tang, Cheng Zhong, Danyang Chen and Jianyi Wang

    Citation: BMC Bioinformatics 2020 21:330

    Content type: Methodology article

    Published on:

  2. Melanoma phenotype and the dynamics underlying its progression are determined by a complex interplay between different types of regulatory molecules. In particular, transcription factors (TFs), microRNAs (miRN...

    Authors: Nivedita Singh, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera and Shailendra K. Gupta

    Citation: BMC Bioinformatics 2020 21:329

    Content type: Research article

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  3. Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole...

    Authors: Vincent Henry, Fatiha Saïs, Olivier Inizan, Elodie Marchadier, Juliette Dibie, Anne Goelzer and Vincent Fromion

    Citation: BMC Bioinformatics 2020 21:327

    Content type: Methodology article

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  4. The three-dimensional (3D) structure of the genome plays a crucial role in gene expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed that the genome is organized in a hierarc...

    Authors: Kellen G. Cresswell, John C. Stansfield and Mikhail G. Dozmorov

    Citation: BMC Bioinformatics 2020 21:319

    Content type: Software

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:373

  5. The pandemic threat of influenza has attracted great attention worldwide. To assist public health decision-makers, new suites of tools are needed to rapidly process and combine viral information retrieved from...

    Authors: Chin-Rur Yang, Chwan-Chuen King, Li-Yu Daisy Liu and Chia-Chi Ku

    Citation: BMC Bioinformatics 2020 21:316

    Content type: Software

    Published on:

  6. Well-characterized biomaterials of high quality have great potential for acceleration and quality improvement in translational biomedical research. To improve accessibility of local sample collections, efforts...

    Authors: Stephanie Heinen, Nick Schulze, Bernd Franke, Florian Klein, Clara Lehmann, Maria J. G. T. Vehreschild, Claas Gloistein, Melanie Stecher and Jörg Janne Vehreschild

    Citation: BMC Bioinformatics 2020 21:290

    Content type: Software

    Published on:

  7. Recognition is an essential function of human beings. Humans easily recognize a person using various inputs such as voice, face, or gesture. In this study, we mainly focus on DL model with multi-modality which...

    Authors: Hyoung-Kyu Song, Ebrahim AlAlkeem, Jaewoong Yun, Tae-Ho Kim, Hyerin Yoo, Dasom Heo, Myungsu Chae and Chan Yeob Yeun

    Citation: BMC Bioinformatics 2020 21:315

    Content type: Research

    Published on:

  8. Recent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a mean...

    Authors: Cinque Soto, Jessica A. Finn, Jordan R. Willis, Samuel B. Day, Robert S. Sinkovits, Taylor Jones, Samuel Schmitz, Jens Meiler, Andre Branchizio and James E. Crowe Jr

    Citation: BMC Bioinformatics 2020 21:314

    Content type: Software

    Published on:

  9. Drug repurposing aims to detect the new therapeutic benefits of the existing drugs and reduce the spent time and cost of the drug development projects. The synthetic repurposing of drugs may prove to be more u...

    Authors: Yosef Masoudi-Sobhanzadeh and Ali Masoudi-Nejad

    Citation: BMC Bioinformatics 2020 21:313

    Content type: Methodology article

    Published on:

  10. Most biomedical information extraction focuses on binary relations within single sentences. However, extracting n-ary relations that span multiple sentences is in huge demand. At present, in the cross-sentence...

    Authors: Di Zhao, Jian Wang, Yijia Zhang, Xin Wang, Hongfei Lin and Zhihao Yang

    Citation: BMC Bioinformatics 2020 21:312

    Content type: Methodology article

    Published on:

  11. Despite continued efforts using chemical similarity methods in virtual screening, currently developed approaches suffer from time-consuming multistep procedures and low success rates. We recently developed a m...

    Authors: Prasannavenkatesh Durai, Young-Joon Ko, Cheol-Ho Pan and Keunwan Park

    Citation: BMC Bioinformatics 2020 21:309

    Content type: Research article

    Published on:

  12. Random forest based variable importance measures have become popular tools for assessing the contributions of the predictor variables in a fitted random forest. In this article we reconsider a frequently used ...

    Authors: Dries Debeer and Carolin Strobl

    Citation: BMC Bioinformatics 2020 21:307

    Content type: Methodology article

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  13. A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection meth...

    Authors: Jane Hung, Allen Goodman, Deepali Ravel, Stefanie C. P. Lopes, Gabriel W. Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj T. Duraisingh, Fabio T. M. Costa, Matthias Marti and Anne E. Carpenter

    Citation: BMC Bioinformatics 2020 21:300

    Content type: Software

    Published on:

  14. 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:

  15. Stable isotope tracing has become an invaluable tool for probing the metabolism of biological systems. However, data analysis and visualization from metabolic tracing studies often involve multiple software pa...

    Authors: Avi Kumar, Jack Mitchener, Zachary A. King and Christian M. Metallo

    Citation: BMC Bioinformatics 2020 21:297

    Content type: Software

    Published on:

  16. 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:

  17. 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:

  18. 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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  19. 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:

  20. 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:

  21. 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:

  22. 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

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  23. 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:

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

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