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  1. Elucidating the modes of action (MoAs) of drugs and drug candidate compounds is critical for guiding translation from drug discovery to clinical application. Despite the development of several data-driven appr...

    Authors: Zhaonan Zou, Michio Iwata, Yoshihiro Yamanishi and Shinya Oki

    Citation: BMC Bioinformatics 2022 23:51

    Content type: Methodology article

    Published on:

  2. Imputation of untyped markers is a standard tool in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy with which genotypes are imp...

    Authors: Albert Rosenberger, Viola Tozzi and Heike Bickeböller

    Citation: BMC Bioinformatics 2022 23:50

    Content type: Research

    Published on:

  3. Fluorescence image analysis in biochemical science often involves the complex tasks of identifying samples for analysis and calculating the desired information from the intensity traces. Analyzing giant unilam...

    Authors: Il-Hyung Lee, Sam Passaro, Selin Ozturk, Juan Ureña and Weitian Wang

    Citation: BMC Bioinformatics 2022 23:48

    Content type: Software

    Published on:

  4. Computational prediction of the interaction between drugs and protein targets is very important for the new drug discovery, as the experimental determination of drug-target interaction (DTI) is expensive and t...

    Authors: Qing Ye, Xiaolong Zhang and Xiaoli Lin

    Citation: BMC Bioinformatics 2022 22(Suppl 12):461

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  5. Bioinformatics is a subject produced by the combination of life science and computer science. It mainly uses computer technology to study the laws of biological systems. The design and realization of DNA circu...

    Authors: Hao Fu, Hui Lv and Qiang Zhang

    Citation: BMC Bioinformatics 2022 22(Suppl 12):437

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  6. Clustering and feature selection act major roles in many communities. As a matrix factorization, Low-Rank Representation (LRR) has attracted lots of attentions in clustering and feature selection, but sometime...

    Authors: Qi Liu

    Citation: BMC Bioinformatics 2022 22(Suppl 12):436

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  7. During the pathogenesisof complex diseases, a sudden health deterioration will occur as results of the cumulative effect of various internal or external factors. The prediction of an early warning signal (pre-...

    Authors: Yanhao Huo, Geng Zhao, Luoshan Ruan, Peng Xu, Gang Fang, Fengyue Zhang, Zhenshen Bao and Xin Li

    Citation: BMC Bioinformatics 2022 22(Suppl 12):367

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  8. The identification of cancer types is of great significance for early diagnosis and clinical treatment of cancer. Clustering cancer samples is an important means to identify cancer types, which has been paid m...

    Authors: Juan Wang, Cong-Hai Lu, Xiang-Zhen Kong, Ling-Yun Dai, Shasha Yuan and Xiaofeng Zhang

    Citation: BMC Bioinformatics 2022 22(Suppl 12):334

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  9. Alkaline earth metal ions are important protein binding ligands in human body, and it is of great significance to predict their binding residues.

    Authors: Kai Sun, Xiuzhen Hu, Zhenxing Feng, Hongbin Wang, Haotian Lv, Ziyang Wang, Gaimei Zhang, Shuang Xu and Xiaoxiao You

    Citation: BMC Bioinformatics 2022 22(Suppl 12):324

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  10. Metagenomics technology can directly extract microbial genetic material from the environmental samples to obtain their sequencing reads, which can be further assembled into contigs through assembly tools. Clus...

    Authors: Zhongjun Jiang, Xiaobo Li and Lijun Guo

    Citation: BMC Bioinformatics 2022 22(Suppl 12):315

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  11. Mining gene regulatory network (GRN) is an important avenue for addressing cancer mechanism. Mutations in cancer genome perturb GRN and cause a rewiring in an orchestrated network. Hence, the exploration of ge...

    Authors: Yijuan Wang and Zhi-Ping Liu

    Citation: BMC Bioinformatics 2022 22(Suppl 12):308

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 12

  12. Recently, with the foundation and development of gene ontology (GO) resources, numerous works have been proposed to compute functional similarity of genes and achieved series of successes in some research fiel...

    Authors: Zhen Tian, Haichuan Fang, Yangdong Ye and Zhenfeng Zhu

    Citation: BMC Bioinformatics 2022 23(Suppl 1):47

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  13. Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional t...

    Authors: Michael Y. Lee, Jacob S. Bedia, Salil S. Bhate, Graham L. Barlow, Darci Phillips, Wendy J. Fantl, Garry P. Nolan and Christian M. Schürch

    Citation: BMC Bioinformatics 2022 23:46

    Content type: Software

    Published on:

  14. Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated usi...

    Authors: Elena Rojano, Fernando M. Jabato, James R. Perkins, José Córdoba-Caballero, Federico García-Criado, Ian Sillitoe, Christine Orengo, Juan A. G. Ranea and Pedro Seoane-Zonjic

    Citation: BMC Bioinformatics 2022 23:43

    Content type: Software

    Published on:

  15. There has been a simultaneous increase in demand and accessibility across genomics, transcriptomics, proteomics and metabolomics data, known as omics data. This has encouraged widespread application of omics d...

    Authors: Mehrdad Mansouri, Sahand Khakabimamaghani, Leonid Chindelevitch and Martin Ester

    Citation: BMC Bioinformatics 2022 23:42

    Content type: Methodology article

    Published on:

  16. DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically e...

    Authors: Maia H. Malonzo, Viivi Halla-aho, Mikko Konki, Riikka J. Lund and Harri Lähdesmäki

    Citation: BMC Bioinformatics 2022 23:41

    Content type: Software

    Published on:

  17. Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart from carrying tandemly repeated DNA, eccDNAs ...

    Authors: Ludwig Mann, Kathrin M. Seibt, Beatrice Weber and Tony Heitkam

    Citation: BMC Bioinformatics 2022 23:40

    Content type: Software

    Published on:

  18. Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making as...

    Authors: Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany and Sol Schvartzman

    Citation: BMC Bioinformatics 2022 23:39

    Content type: Software

    Published on:

  19. Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulat...

    Authors: Emily Kaczmarek, Jina Nanayakkara, Alireza Sedghi, Mehran Pesteie, Thomas Tuschl, Neil Renwick and Parvin Mousavi

    Citation: BMC Bioinformatics 2022 23:38

    Content type: Research

    Published on:

  20. LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecu...

    Authors: Jeremy J. Yang, Christopher R. Gessner, Joel L. Duerksen, Daniel Biber, Jessica L. Binder, Murat Ozturk, Brian Foote, Robin McEntire, Kyle Stirling, Ying Ding and David J. Wild

    Citation: BMC Bioinformatics 2022 23:37

    Content type: Methodology article

    Published on:

  21. With the precision of the mass spectrometry (MS) going higher, the MS file size increases rapidly. Beyond the widely-used open format mzML, near-lossless or lossless compression algorithms and formats emerged ...

    Authors: Miaoshan Lu, Shaowei An, Ruimin Wang, Jinyin Wang and Changbin Yu

    Citation: BMC Bioinformatics 2022 23:35

    Content type: Software

    Published on:

  22. Compound–protein interaction prediction is necessary to investigate health regulatory functions and promotes drug discovery. Machine learning is becoming increasingly important in bioinformatics for applicatio...

    Authors: Ermal Elbasani, Soualihou Ngnamsie Njimbouom, Tae-Jin Oh, Eung-Hee Kim, Hyun Lee and Jeong-Dong Kim

    Citation: BMC Bioinformatics 2022 22(Suppl 5):616

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  23. Researchers have attempted to apply deep learning methods of artificial intelligence for rapidly and accurately detecting acute lymphoblastic leukemia (ALL) in microscopic images.

    Authors: Yao-Mei Chen, Fu-I Chou, Wen-Hsien Ho and Jinn-Tsong Tsai

    Citation: BMC Bioinformatics 2022 22(Suppl 5):615

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  24. Drug combination, offering an insight into the increased therapeutic efficacy and reduced toxicity, plays an essential role in the therapy of many complex diseases. Although significant efforts have been devot...

    Authors: Fei Song, Shiyin Tan, Zengfa Dou, Xiaogang Liu and Xiaoke Ma

    Citation: BMC Bioinformatics 2022 23(Suppl 1):34

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  25. Representations of the relationships among data using networks are widely used in several research fields such as computational biology, medical informatics and social network mining. Recently, complex network...

    Authors: Pietro Hiram Guzzi, Giuseppe Tradigo and Pierangelo Veltri

    Citation: BMC Bioinformatics 2022 22(Suppl 15):614

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 15

  26. Glucocorticoid-remediable aldosteronism (GRA) is a form of heritable hypertension caused by a chimeric fusion resulting from unequal crossing over between 11β‐hydroxylase (CYP11B1) and aldosterone synthase (CYP11...

    Authors: Yu-Ching Wu, Chia-I Chen, Peng-Ying Chen, Chun-Hung Kuo, Yi-Hsuan Hung, Kang-Yung Peng, Vin-Cent Wu, Jyy-Jih Tsai-Wu and Chia-Lang Hsu

    Citation: BMC Bioinformatics 2022 22(Suppl 10):613

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  27. Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However...

    Authors: Xiong Yuan, Zirong Li, Liwen Xiong, Sufeng Song, Xingfei Zheng, Zhonghai Tang, Zheming Yuan and Lanzhi Li

    Citation: BMC Bioinformatics 2022 23:30

    Content type: Research

    Published on:

  28. DNA methylation has long been known as an epigenetic gene silencing mechanism. For a motivating example, the methylomes of cancer and non-cancer cells show a number of methylation differences, indicating that ...

    Authors: Xifang Sun, Donglin Wang, Jiaqiang Zhu and Shiquan Sun

    Citation: BMC Bioinformatics 2022 23(Suppl 1):29

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 23 Supplement 1

  29. Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, ana...

    Authors: Xuemin Dong, Shanshan Dong, Shengkai Pan and Xiangjiang Zhan

    Citation: BMC Bioinformatics 2022 23:26

    Content type: Software

    Published on:

  30. Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parame...

    Authors: Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik and Somali Chaterji

    Citation: BMC Bioinformatics 2022 23:25

    Content type: Methodology article

    Published on:

  31. As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also to develop better treatment strategies using existing drugs to ...

    Authors: Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen and Pia Abel zur Wiesch

    Citation: BMC Bioinformatics 2022 23:22

    Content type: Software

    Published on:

  32. Next-generation sequencing (NGS) is nowadays the most used high-throughput technology for DNA sequencing. Among others NGS enables the in-depth analysis of immune repertoires. Research in the field of T cell r...

    Authors: Julia Vetter, Susanne Schaller, Andreas Heinzel, Constantin Aschauer, Roman Reindl-Schwaighofer, Kira Jelencsics, Karin Hu, Rainer Oberbauer and Stephan M. Winkler

    Citation: BMC Bioinformatics 2022 23:21

    Content type: Software

    Published on:

  33. A limitation of traditional differential expression analysis on small datasets involves the possibility of false positives and false negatives due to sample variation. Considering the recent advances in deep l...

    Authors: Tulika Kakati, Dhruba K. Bhattacharyya, Jugal K. Kalita and Trina M. Norden-Krichmar

    Citation: BMC Bioinformatics 2022 23:17

    Content type: Methodology article

    Published on:

  34. Single-cell RNA sequencing is becoming a powerful tool to identify cell states, reconstruct developmental trajectories, and deconvolute spatial expression. The rapid development of computational methods promot...

    Authors: Huijian Feng, Lihui Lin and Jiekai Chen

    Citation: BMC Bioinformatics 2022 23:16

    Content type: Software

    Published on:

  35. RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs,...

    Authors: Albert E. Zhou, Zalak V. Shah, Katie R. Bradwell, James B. Munro, Andrea A. Berry, David Serre, Shannon Takala-Harrison, Timothy D. O’Connor, Joana C. Silva and Mark A. Travassos

    Citation: BMC Bioinformatics 2022 23:15

    Content type: Software

    Published on:

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