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  1. ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and a...

    Authors: Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan

    Citation: BMC Bioinformatics 2021 22:193

    Content type: Methodology article

    Published on:

  2. The Cox proportional hazards model is commonly used to predict hazard ratio, which is the risk or probability of occurrence of an event of interest. However, the Cox proportional hazard model cannot directly g...

    Authors: Eu-Tteum Baek, Hyung Jeong Yang, Soo Hyung Kim, Guee Sang Lee, In-Jae Oh, Sae-Ryung Kang and Jung-Joon Min

    Citation: BMC Bioinformatics 2021 22:192

    Content type: Methodology article

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  3. Harmonin Homogy Domains (HHD) are recently identified orphan domains of about 70 residues folded in a compact five alpha-helix bundle that proved to be versatile in terms of function, allowing for direct bindi...

    Authors: Baptiste Colcombet-Cazenave, Karen Druart, Crystel Bonnet, Christine Petit, Olivier Spérandio, Julien Guglielmini and Nicolas Wolff

    Citation: BMC Bioinformatics 2021 22:190

    Content type: Research article

    Published on:

  4. We previously developed TANTIGEN, a comprehensive online database cataloging more than 1000 T cell epitopes and HLA ligands from 292 tumor antigens. In TANTIGEN 2.0, we significantly expanded coverage in both ...

    Authors: Guanglan Zhang, Lou Chitkushev, Lars Rønn Olsen, Derin B. Keskin and Vladimir Brusic

    Citation: BMC Bioinformatics 2021 22(Suppl 8):40

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 8

  5. Despite the importance of alternative poly-adenylation and 3′ UTR length for a variety of biological phenomena, there are limited means of detecting UTR changes from standard transcriptomic data.

    Authors: Stefan Gerber, Gerhard Schratt and Pierre-Luc Germain

    Citation: BMC Bioinformatics 2021 22:189

    Content type: Methodology article

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  6. The genomics data analysis has been widely used to study disease genes and drug targets. However, the existence of missing values in genomics datasets poses a significant problem, which severely hinders the us...

    Authors: Xinshan Zhu, Jiayu Wang, Biao Sun, Chao Ren, Ting Yang and Jie Ding

    Citation: BMC Bioinformatics 2021 22:188

    Content type: Methodology article

    Published on:

  7. Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data become useful for modeling entities and interactions in biological and simi...

    Authors: Khushnood Abbas, Alireza Abbasi, Shi Dong, Ling Niu, Laihang Yu, Bolun Chen, Shi-Min Cai and Qambar Hasan

    Citation: BMC Bioinformatics 2021 22:187

    Content type: Research article

    Published on:

  8. Clustering is a crucial step in the analysis of single-cell data. Clusters identified in an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, super...

    Authors: Bobby Ranjan, Florian Schmidt, Wenjie Sun, Jinyu Park, Mohammad Amin Honardoost, Joanna Tan, Nirmala Arul Rayan and Shyam Prabhakar

    Citation: BMC Bioinformatics 2021 22:186

    Content type: Methodology article

    Published on:

  9. Microsatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite leng...

    Authors: Tao Zhou, Libin Chen, Jing Guo, Mengmeng Zhang, Yanrui Zhang, Shanbo Cao, Feng Lou and Haijun Wang

    Citation: BMC Bioinformatics 2021 22:185

    Content type: Software

    Published on:

  10. The interactions of proteins are determined by their sequences and affect the regulation of the cell cycle, signal transduction and metabolism, which is of extraordinary significance to modern proteomics resea...

    Authors: Yang Wang, Zhanchao Li, Yanfei Zhang, Yingjun Ma, Qixing Huang, Xingyu Chen, Zong Dai and Xiaoyong Zou

    Citation: BMC Bioinformatics 2021 22:184

    Content type: Research article

    Published on:

  11. The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromos...

    Authors: Haipeng Xing, Yingru Wu, Michael Q. Zhang and Yong Chen

    Citation: BMC Bioinformatics 2021 22:183

    Content type: Methodology article

    Published on:

  12. The rapid spread of the COVID-19 demands immediate response from the scientific communities. Appropriate countermeasures mean thoughtful and educated choice of viral targets (epitopes). There are several artic...

    Authors: Aleksandra Gruca, Joanna Ziemska-Legiecka, Patryk Jarnot, Elzbieta Sarnowska, Tomasz J. Sarnowski and Marcin Grynberg

    Citation: BMC Bioinformatics 2021 22:182

    Content type: Research article

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  13. The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remai...

    Authors: Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, Jennifer J. Johnston and Leslie G. Biesecker

    Citation: BMC Bioinformatics 2021 22:181

    Content type: Methodology article

    Published on:

  14. Permutation testing is often considered the “gold standard” for multi-test significance analysis, as it is an exact test requiring few assumptions about the distribution being computed. However, it can be comp...

    Authors: James M. Kunert-Graf, Nikita A. Sakhanenko and David J. Galas

    Citation: BMC Bioinformatics 2021 22:180

    Content type: Methodology article

    Published on:

  15. The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past ...

    Authors: Gnanendra Shanmugam, Song Hee Lee and Junhyun Jeon

    Citation: BMC Bioinformatics 2021 22:179

    Content type: Software

    Published on:

  16. The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment of reads by denoising or by clustering methods, ...

    Authors: Adrià Antich, Creu Palacin, Owen S. Wangensteen and Xavier Turon

    Citation: BMC Bioinformatics 2021 22:177

    Content type: Research article

    Published on:

  17. For multivariate data analysis involving only two input matrices (e.g., X and Y), the previously published methods for variable influence on projection (e.g., VIPOPLS or VIPO2PLS) are widely used for variable sel...

    Authors: Beatriz Galindo-Prieto, Paul Geladi and Johan Trygg

    Citation: BMC Bioinformatics 2021 22:176

    Content type: Methodology article

    Published on:

  18. Identifying lncRNA-disease associations not only helps to better comprehend the underlying mechanisms of various human diseases at the lncRNA level but also speeds up the identification of potential biomarkers...

    Authors: Rong Zhu, Yong Wang, Jin-Xing Liu and Ling-Yun Dai

    Citation: BMC Bioinformatics 2021 22:175

    Content type: Methodology article

    Published on:

  19. Supervised learning from high-throughput sequencing data presents many challenges. For one, the curse of dimensionality often leads to overfitting as well as issues with scalability. This can bring about inacc...

    Authors: Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford and Christopher J. Langmead

    Citation: BMC Bioinformatics 2021 22:174

    Content type: Methodology article

    Published on:

  20. To address the need for easy and reliable species classification in plant genetic resources collections, we assessed the potential of five classifiers (Random Forest, Neighbour-Joining, 1-Nearest Neighbour, a ...

    Authors: Artur van Bemmelen van der Plaat, Rob van Treuren and Theo J. L. van Hintum

    Citation: BMC Bioinformatics 2021 22:173

    Content type: Research article

    Published on:

  21. Protein post-translational modification (PTM) is a key issue to investigate the mechanism of protein’s function. With the rapid development of proteomics technology, a large amount of protein sequence data has...

    Authors: Yingxi Yang, Hui Wang, Wen Li, Xiaobo Wang, Shizhao Wei, Yulong Liu and Yan Xu

    Citation: BMC Bioinformatics 2021 22:171

    Content type: Research article

    Published on:

  22. The most common measure of association between two continuous variables is the Pearson correlation (Maronna et al. in Safari an OMC. Robust statistics, 2019. https://login.proxy.bib.uottawa.ca/login?url=https:...

    Authors: Mohammad Tabatabai, Stephanie Bailey, Zoran Bursac, Habib Tabatabai, Derek Wilus and Karan P. Singh

    Citation: BMC Bioinformatics 2021 22:170

    Content type: Methodology article

    Published on:

  23. Studies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life activities and complex diseases. RNA secondary structure profile can re...

    Authors: Linyu Wang, Xiaodan Zhong, Shuo Wang, Hao Zhang and Yuanning Liu

    Citation: BMC Bioinformatics 2021 22:169

    Content type: Research article

    Published on:

  24. Hepatocellular carcinoma (HCC), derived from hepatocytes, is the main histological subtype of primary liver cancer and poses a serious threat to human health due to the high incidence and poor prognosis. This stu...

    Authors: Qinghong Dai, Tao Liu, Yongchao Gao, Honghao Zhou, Xiong Li and Wei Zhang

    Citation: BMC Bioinformatics 2021 22:167

    Content type: Research article

    Published on:

  25. Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often bas...

    Authors: The Tien Mai, Paul Turner and Jukka Corander

    Citation: BMC Bioinformatics 2021 22:164

    Content type: Research article

    Published on:

  26. Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in...

    Authors: Sondes Haddad-Boubaker, Houcemeddine Othman, Rabeb Touati, Kaouther Ayouni, Marwa Lakhal, Imen Ben Mustapha, Kais Ghedira, Maher Kharrat and Henda Triki

    Citation: BMC Bioinformatics 2021 22:163

    Content type: Research article

    Published on:

  27. Cumulative evidence from biological experiments has confirmed that miRNAs have significant roles to diagnose and treat complex diseases. However, traditional medical experiments have limitations in time-consum...

    Authors: Bailong Liu, Xiaoyan Zhu, Lei Zhang, Zhizheng Liang and Zhengwei Li

    Citation: BMC Bioinformatics 2021 22:161

    Content type: Research article

    Published on:

  28. Deep immune receptor sequencing, RepSeq, provides unprecedented opportunities for identifying and studying condition-associated T-cell clonotypes, represented by T-cell receptor (TCR) CDR3 sequences. However, ...

    Authors: Dawit A. Yohannes, Katri Kaukinen, Kalle Kurppa, Päivi Saavalainen and Dario Greco

    Citation: BMC Bioinformatics 2021 22:159

    Content type: Methodology article

    Published on:

  29. 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:

  30. Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell ...

    Authors: Andrew J. Kavran and Aaron Clauset

    Citation: BMC Bioinformatics 2021 22:157

    Content type: Research article

    Published on:

  31. A growing body of evidence has shown the association between tuberculosis (TB) infection and lung cancer. However, the possible effect of strain‐specific behavior of Mycobacterium tuberculosis (M.tb) population, ...

    Authors: Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat and Farzam Vaziri

    Citation: BMC Bioinformatics 2021 22:154

    Content type: Research article

    Published on:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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

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  38. 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:

  39. 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:

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