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  1. 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:

  2. 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

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  3. 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:

  4. 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

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  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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

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  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. Matrix factorization methods are linear models, with limited capability to model complex relations. In our work, we use tropical semiring to introduce non-linearity into matrix factorization models. We propose...

    Authors: Amra Omanović, Hilal Kazan, Polona Oblak and Tomaž Curk

    Citation: BMC Bioinformatics 2021 22:89

    Content type: Research article

    Published on:

  27. Microbes perform a fundamental economic, social, and environmental role in our society. Metagenomics makes it possible to investigate microbes in their natural environments (the complex communities) and their ...

    Authors: Raíssa Silva, Kleber Padovani, Fabiana Góes and Ronnie Alves

    Citation: BMC Bioinformatics 2021 22:87

    Content type: Software

    Published on:

  28. The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting thes...

    Authors: Camilo Broc, Therese Truong and Benoit Liquet

    Citation: BMC Bioinformatics 2021 22:86

    Content type: Methodology article

    Published on:

  29. Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortiu...

    Authors: Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, Michael P. Snyder and Euan A. Ashley

    Citation: BMC Bioinformatics 2021 22:85

    Content type: Methodology article

    Published on:

  30. Single-cell RNA-seq (scRNA-seq) enables the profiling of genome-wide gene expression at the single-cell level and in so doing facilitates insight into and information about cellular heterogeneity within a tiss...

    Authors: Matthew N. Bernstein, Zijian Ni, Michael Collins, Mark E. Burkard, Christina Kendziorski and Ron Stewart

    Citation: BMC Bioinformatics 2021 22:83

    Content type: Software

    Published on:

  31. Immunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are ...

    Authors: Anna Maria Masci, Scott White, Ben Neely, Maryanne Ardini-Polaske, Carol B. Hill, Ravi S. Misra, Bruce Aronow, Nathan Gaddis, Lina Yang, Susan E. Wert, Scott M. Palmer and Cliburn Chan

    Citation: BMC Bioinformatics 2021 22:82

    Content type: Methodology article

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  32. A wide range of bioactive compounds is produced by enzymes and enzymatic complexes encoded in biosynthetic gene clusters (BGCs). These BGCs can be identified and functionally annotated based on their DNA seque...

    Authors: Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel and Eivind Almaas

    Citation: BMC Bioinformatics 2021 22:81

    Content type: Research article

    Published on:

  33. One goal of multi-omic studies is to identify interpretable predictive models for outcomes of interest, with analytes drawn from multiple omes. Such findings could support refined biological insight and hypoth...

    Authors: Janet C. Siebert, Martine Saint-Cyr, Sarah J. Borengasser, Brandie D. Wagner, Catherine A. Lozupone and Carsten Görg

    Citation: BMC Bioinformatics 2021 22:80

    Content type: Research article

    Published on:

  34. Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard me...

    Authors: Dörte Wittenburg, Michael Doschoris and Jan Klosa

    Citation: BMC Bioinformatics 2021 22:79

    Content type: Research article

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  35. The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast an...

    Authors: Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gian Vincenzo Zuccotti and Francesco Comandatore

    Citation: BMC Bioinformatics 2021 22:76

    Content type: Software

    Published on:

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