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  1. Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone ...

    Authors: Lidong Guo, Mengyang Xu, Wenchao Wang, Shengqiang Gu, Xia Zhao, Fang Chen, Ou Wang, Xun Xu, Inge Seim, Guangyi Fan, Li Deng and Xin Liu
    Citation: BMC Bioinformatics 2021 22:158
    Content type: Software Published on:

  3. Recent studies have confirmed that N7-methylguanosine (m7G) modification plays an important role in regulating various biological processes and has associations with multiple diseases. Wet-lab experiments are cos...

    Authors: Jiani Ma, Lin Zhang, Jin Chen, Bowen Song, Chenxuan Zang and Hui Liu
    Citation: BMC Bioinformatics 2021 22:152
    Content type: Software Published on:

  4. A number of predictive models for aquatic toxicity are available, however, the accuracy and extent of easy to use of these in silico tools in risk assessment still need further studied. This study evaluated th...

    Authors: Linjun Zhou, Deling Fan, Wei Yin, Wen Gu, Zhen Wang, Jining Liu, Yanhua Xu, Lili Shi, Mingqing Liu and Guixiang Ji
    Citation: BMC Bioinformatics 2021 22:151
    Content type: Research article Published on:

  5. Currently, no proven effective drugs for the novel coronavirus disease COVID-19 exist and despite widespread vaccination campaigns, we are far short from herd immunity. The number of people who are still vulne...

    Authors: Giulia Fiscon and Paola Paci
    Citation: BMC Bioinformatics 2021 22:150
    Content type: Software Published on:

  6. A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost an...

    Authors: Zhong Ren, Gundula Povysil, Joseph A. Hostyk, Hongzhu Cui, Nitin Bhardwaj and David B. Goldstein
    Citation: BMC Bioinformatics 2021 22:149
    Content type: Software Published on:

  8. Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the deter...

    Authors: Martin Lyčka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jiří Fajkus and Miloslava Fojtová
    Citation: BMC Bioinformatics 2021 22:145
    Content type: Software Published on:

  9. Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technolo...

    Authors: Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo and Raffaele Giancarlo
    Citation: BMC Bioinformatics 2021 22:144
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:73

  12. Spliced leader (SL) trans-splicing replaces the 5′ end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential f...

    Authors: Marius A. Wenzel, Berndt Müller and Jonathan Pettitt
    Citation: BMC Bioinformatics 2021 22:140
    Content type: Software Published on:

  13. The rapidly increasing dimensionality and throughput of flow and mass cytometry data necessitate new bioinformatics tools for analysis and interpretation, and the recently emerging single-cell-based algorithms...

    Authors: Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Weili Zhao, Xiao-Jian Sun and Jinyan Huang
    Citation: BMC Bioinformatics 2021 22:138
    Content type: Research article Published on:

  14. Flow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell...

    Authors: Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish and Susan Holmes
    Citation: BMC Bioinformatics 2021 22:137
    Content type: Research article Published on:

  15. Numerous studies have demonstrated that long non-coding RNAs are related to plenty of human diseases. Therefore, it is crucial to predict potential lncRNA-disease associations for disease prognosis, diagnosis ...

    Authors: Zhuangwei Shi, Han Zhang, Chen Jin, Xiongwen Quan and Yanbin Yin
    Citation: BMC Bioinformatics 2021 22:136
    Content type: Research article Published on:

  17. Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pa...

    Authors: Tuure Hameri, Georgios Fengos and Vassily Hatzimanikatis
    Citation: BMC Bioinformatics 2021 22:134
    Content type: Methodology article Published on:

  18. Non-coding RNA (ncRNA) and protein interactions play essential roles in various physiological and pathological processes. The experimental methods used for predicting ncRNA–protein interactions are time-consum...

    Authors: Jingjing Wang, Yanpeng Zhao, Weikang Gong, Yang Liu, Mei Wang, Xiaoqian Huang and Jianjun Tan
    Citation: BMC Bioinformatics 2021 22:133
    Content type: Research article Published on:

  19. Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made us...

    Authors: Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa and Tomoyuki Hiroyasu
    Citation: BMC Bioinformatics 2021 22:132
    Content type: Methodology article Published on:

  20. Nowadays, multiple omics data are measured on the same samples in the belief that these different omics datasets represent various aspects of the underlying biological systems. Integrating these omics datasets...

    Authors: Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat and Hae-Won Uh
    Citation: BMC Bioinformatics 2021 22:131
    Content type: Methodology article Published on:

  22. Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem...

    Authors: Liangliang Zhang, Yushu Shi, Kim-Anh Do, Christine B. Peterson and Robert R. Jenq
    Citation: BMC Bioinformatics 2021 22:126
    Content type: Methodology article Published on:

  26. Trauma-induced coagulopathy (TIC) is a disorder that occurs in one-third of severely injured trauma patients, manifesting as increased bleeding and a 4X risk of mortality. Understanding the mechanisms driving ...

    Authors: Richard M. Jiang, Arya A. Pourzanjani, Mitchell J. Cohen and Linda Petzold
    Citation: BMC Bioinformatics 2021 22:122
    Content type: Research article Published on:

  27. The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources. Pfam is possibly the most well known prote...

    Authors: Elena Tea Russo, Alessandro Laio and Marco Punta
    Citation: BMC Bioinformatics 2021 22:121
    Content type: Methodology article Published on:

  28. Recently, copy number variations (CNV) impacting genes involved in oncogenic pathways have attracted an increasing attention to manage disease susceptibility. CNV is one of the most important somatic aberratio...

    Authors: Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Elodie Bohers, Nicolas Vergne, Caroline Berard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal…
    Citation: BMC Bioinformatics 2021 22:120
    Content type: Methodology article Published on:

  30. Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of ant...

    Authors: Xiao Liang, Kyle Akers, Ishi Keenum, Lauren Wind, Suraj Gupta, Chaoqi Chen, Reem Aldaihani, Amy Pruden, Liqing Zhang, Katharine F. Knowlton, Kang Xia and Lenwood S. Heath
    Citation: BMC Bioinformatics 2021 22:117
    Content type: Software Published on:

  31. Correlation network analysis has become an integral tool to study metabolite datasets. Networks are constructed by omitting correlations between metabolites based on two thresholds—namely the r and the associated...

    Authors: David Toubiana and Helena Maruenda
    Citation: BMC Bioinformatics 2021 22:116
    Content type: Methodology article Published on:

  34. Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. ...

    Authors: Kevin De Angeli, Shang Gao, Mohammed Alawad, Hong-Jun Yoon, Noah Schaefferkoetter, Xiao-Cheng Wu, Eric B. Durbin, Jennifer Doherty, Antoinette Stroup, Linda Coyle, Lynne Penberthy and Georgia Tourassi
    Citation: BMC Bioinformatics 2021 22:113
    Content type: Research article Published on:

  35. Manual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the “gold standard” for malaria diagnosis. One of the drawbacks of this method is that its accuracy, consistency, a...

    Authors: Fetulhak Abdurahman, Kinde Anlay Fante and Mohammed Aliy
    Citation: BMC Bioinformatics 2021 22:112
    Content type: Research article Published on:

  36. Machine learning involves strategies and algorithms that may assist bioinformatics analyses in terms of data mining and knowledge discovery. In several applications, viz. in Life Sciences, it is often more imp...

    Authors: Mateusz Garbulowski, Klev Diamanti, Karolina Smolińska, Nicholas Baltzer, Patricia Stoll, Susanne Bornelöv, Aleksander Øhrn, Lars Feuk and Jan Komorowski
    Citation: BMC Bioinformatics 2021 22:110
    Content type: Software Published on:

  38. Knowledge on the molecular targets of diseases and drugs is crucial for elucidating disease pathogenesis and mechanism of action of drugs, and for driving drug discovery and treatment formulation. In this rega...

    Authors: Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker and Rudiyanto Gunawan
    Citation: BMC Bioinformatics 2021 22:108
    Content type: Methodology article Published on:

  39. Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for ...

    Authors: Jakob Willforss, Valentina Siino and Fredrik Levander
    Citation: BMC Bioinformatics 2021 22:107
    Content type: Software Published on:

  40. VCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinic...

    Authors: Robert H. Dolin, Shaileshbhai R. Gothi, Aziz Boxwala, Bret S. E. Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby, Varun Suraj, Ning Xie, Srikar Chamala and Gil Alterovitz
    Citation: BMC Bioinformatics 2021 22:104
    Content type: Software Published on:

  42. Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the...

    Authors: Umesh Kathad, Aditya Kulkarni, Joseph Ryan McDermott, Jordan Wegner, Peter Carr, Neha Biyani, Rama Modali, Jean-Philippe Richard, Panna Sharma and Kishor Bhatia
    Citation: BMC Bioinformatics 2021 22:102
    Content type: Research article Published on:

  43. The rapid expansion of the CRISPR toolbox through tagging effector domains to either enzymatically inactive Cas9 (dCas9) or Cas9 nickase (nCas9) has led to several promising new gene editing strategies. Recent...

    Authors: Sebastian M. Siegner, Mehmet E. Karasu, Markus S. Schröder, Zacharias Kontarakis and Jacob E. Corn
    Citation: BMC Bioinformatics 2021 22:101
    Content type: Software Published on:

  44. There have been many recent breakthroughs in processing and analyzing large-scale data sets in biomedical informatics. For example, the CytoGPS algorithm has enabled the use of text-based karyotypes by transfo...

    Authors: Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo and Kevin R. Coombes
    Citation: BMC Bioinformatics 2021 22:100
    Content type: Software Published on:

  45. Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including p...

    Authors: Casey B. Bernhards, Matthew W. Lux, Sarah E. Katoski, Tyler D. P. Goralski, Alvin T. Liem and Henry S. Gibbons
    Citation: BMC Bioinformatics 2021 22:98
    Content type: Methodology article Published on:

  46. The accumulation of various multi-omics data and computational approaches for data integration can accelerate the development of precision medicine. However, the algorithm development for multi-omics data inte...

    Authors: Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He and Xiaochen Bo
    Citation: BMC Bioinformatics 2021 22:97
    Content type: Methodology article Published on:

  49. To effectively detect and investigate various cell-related diseases, it is essential to understand cell behaviour. The ability to detection mitotic cells is a fundamental step in diagnosing cell-related diseas...

    Authors: Titinunt Kitrungrotsakul, Yutaro Iwamoto, Satoko Takemoto, Hideo Yokota, Sari Ipponjima, Tomomi Nemoto, Lanfen Lin, Ruofeng Tong, Jingsong Li and Yen-Wei Chen
    Citation: BMC Bioinformatics 2021 22:91
    Content type: Research article Published on:

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