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  1. Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools...

    Authors: Fajin Li, Xudong Xing, Zhengtao Xiao, Gang Xu and Xuerui Yang

    Citation: BMC Bioinformatics 2020 21:340

    Content type: Software

    Published on:

  2. It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting l...

    Authors: Wenwen Fan, Junliang Shang, Feng Li, Yan Sun, Shasha Yuan and Jin-Xing Liu

    Citation: BMC Bioinformatics 2020 21:339

    Content type: Methodology article

    Published on:

  3. Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functi...

    Authors: Anthony R. Soltis, Clifton L. Dalgard, Harvey B. Pollard and Matthew D. Wilkerson

    Citation: BMC Bioinformatics 2020 21:338

    Content type: Software

    Published on:

  4. Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow ...

    Authors: Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin and Michael E. Douglas

    Citation: BMC Bioinformatics 2020 21:337

    Content type: Software

    Published on:

  5. Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network gr...

    Authors: Henri Riihimäki, Wojciech Chachólski, Jakob Theorell, Jan Hillert and Ryan Ramanujam

    Citation: BMC Bioinformatics 2020 21:336

    Content type: Research article

    Published on:

  6. The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the bree...

    Authors: Behrend Heeren, Stefan Paulus, Heiner Goldbach, Heiner Kuhlmann, Anne-Katrin Mahlein, Martin Rumpf and Benedikt Wirth

    Citation: BMC Bioinformatics 2020 21:335

    Content type: Research article

    Published on:

  7. Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assemble...

    Authors: Yi Yue, Hao Huang, Zhao Qi, Hui-Min Dou, Xin-Yi Liu, Tian-Fei Han, Yue Chen, Xiang-Jun Song, You-Hua Zhang and Jian Tu

    Citation: BMC Bioinformatics 2020 21:334

    Content type: Research article

    Published on:

  8. Gene expression signatures for the prediction of differential survival of patients undergoing anti-cancer therapies are of great interest because they can be used to prospectively stratify patients entering ne...

    Authors: Joachim Theilhaber, Marielle Chiron, Jennifer Dreymann, Donald Bergstrom and Jack Pollard

    Citation: BMC Bioinformatics 2020 21:333

    Content type: Methodology article

    Published on:

  9. Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correctio...

    Authors: Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov and Sergey Nurk

    Citation: BMC Bioinformatics 2020 21(Suppl 12):306

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  10. Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes t...

    Authors: Maria A. Daugavet, Sergey V. Shabelnikov and Olga I. Podgornaya

    Citation: BMC Bioinformatics 2020 21(Suppl 12):305

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  11. The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares contro...

    Authors: Gennady V. Khvorykh and Andrey V. Khrunin

    Citation: BMC Bioinformatics 2020 21(Suppl 12):304

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  12. Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis...

    Authors: Yulia Kondratenko, Anton Korobeynikov and Alla Lapidus

    Citation: BMC Bioinformatics 2020 21(Suppl 12):303

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

    The Correction to this article has been published in BMC Bioinformatics 2020 21:362

  13. De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impos...

    Authors: Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale and Alla Lapidus

    Citation: BMC Bioinformatics 2020 21(Suppl 12):302

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  14. 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:

  15. 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

    Published on:

  16. Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds)...

    Authors: Arne Kutzner, Pok-Son Kim and Markus Schmidt

    Citation: BMC Bioinformatics 2020 21:328

    Content type: Methodology article

    Published on:

  17. 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

    Published on:

  18. 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

  19. 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:

  20. 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:

  21. 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:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:421

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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

    Published on:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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

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