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  1. A recurring problem in image segmentation is a lack of labelled data. This problem is especially acute in the segmentation of lung computed tomography (CT) of patients with Coronavirus Disease 2019 (COVID-19)....

    Authors: Judah Zammit, Daryl L. X. Fung, Qian Liu, Carson Kai-Sang Leung and Pingzhao Hu
    Citation: BMC Bioinformatics 2022 23(Suppl 7):343

    This article is part of a Supplement: Volume 23 Supplement 7

  2. Gene regulatory networks have garnered a large amount of attention to understand disease mechanisms caused by complex molecular network interactions. These networks have been applied to predict specific clinic...

    Authors: Heewon Park, Seiya Imoto and Satoru Miyano
    Citation: BMC Bioinformatics 2022 23:342
  3. Cancer is a heterogeneous disease in which tumor genes cooperate as well as adapt and evolve to the changing conditions for individual patients. It is a meaningful task to discover the personalized cancer driv...

    Authors: Shao-Wu Zhang, Zhen-Nan Wang, Yan Li and Wei-Feng Guo
    Citation: BMC Bioinformatics 2022 23:341
  4. Cells progressing from an early state to a developed state give rise to lineages in cell differentiation. Knowledge of these lineages is central to developmental biology. Each biological lineage corresponds to...

    Authors: Lovemore Tenha and Mingzhou Song
    Citation: BMC Bioinformatics 2022 23(Suppl 8):340

    This article is part of a Supplement: Volume 23 Supplement 8

  5. Essential proteins are indispensable to the development and survival of cells. The identification of essential proteins not only is helpful for the understanding of the minimal requirements for cell survival, ...

    Authors: Weixia Xu, Yunfeng Dong, Jihong Guan and Shuigeng Zhou
    Citation: BMC Bioinformatics 2022 23(Suppl 8):339

    This article is part of a Supplement: Volume 23 Supplement 8

  6. Extraction of drug drug interactions from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Exist...

    Authors: Biao Duan, Jing Peng and Yi Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 7):338

    This article is part of a Supplement: Volume 23 Supplement 7

  7. Single-cell RNA sequencing (scRNA-seq) technologies offer unique opportunities for exploring heterogeneous cell populations. However, in-depth single-cell transcriptomic characterization of complex tissues oft...

    Authors: Mariia Bilous, Loc Tran, Chiara Cianciaruso, Aurélie Gabriel, Hugo Michel, Santiago J. Carmona, Mikael J. Pittet and David Gfeller
    Citation: BMC Bioinformatics 2022 23:336
  8. Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensi...

    Authors: Daniel Wüstner
    Citation: BMC Bioinformatics 2022 23:334
  9. Influenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are known to be responsible for a number of pandemics. A key computational is...

    Authors: Yixiang Zhang, Kent M. Eskridge, Shunpu Zhang and Guoqing Lu
    Citation: BMC Bioinformatics 2022 23:333
  10. Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can ...

    Authors: Morteza Kouhsar, Esra Kashaninia, Behnam Mardani and Hamid R. Rabiee
    Citation: BMC Bioinformatics 2022 23:331
  11. Biological data suffers from noise that is inherent in the measurements. This is particularly true for time-series gene expression measurements. Nevertheless, in order to to explore cellular dynamics, scientis...

    Authors: Nadav Bar, Bahareh Nikparvar, Naresh Doni Jayavelu and Fabienne Krystin Roessler
    Citation: BMC Bioinformatics 2022 23:330
  12. The treatment and prognosis of lung adenocarcinoma (LUAD) remains a challenge. The study aimed to conduct a systematic analysis of the predictive capacity of N6-methyladenosine (m6A)-related long non-coding RN...

    Authors: Chen Gao, Ning Kong, Fan Zhang, Liuzhi Zhou, Maosheng Xu and Linyu Wu
    Citation: BMC Bioinformatics 2022 23:327
  13. The malaria risk prediction is currently limited to using advanced statistical methods, such as time series and cluster analysis on epidemiological data. Nevertheless, machine learning models have been explore...

    Authors: Kah Yee Tai, Jasbir Dhaliwal and KokSheik Wong
    Citation: BMC Bioinformatics 2022 23:325
  14. Applying directed acyclic graph (DAG) models to proteogenomic data has been shown effective for detecting causal biomarkers of complex diseases. However, there remain unsolved challenges in DAG learning to joi...

    Authors: Shrabanti Chowdhury, Ru Wang, Qing Yu, Catherine J. Huntoon, Larry M. Karnitz, Scott H. Kaufmann, Steven P. Gygi, Michael J. Birrer, Amanda G. Paulovich, Jie Peng and Pei Wang
    Citation: BMC Bioinformatics 2022 23:321
  15. Visceral Leishmaniasis (VL) is a fatal vector-borne parasitic disorder occurring mainly in tropical and subtropical regions. VL falls under the category of neglected tropical diseases with growing drug resista...

    Authors: Subhadip Saha, Shubham Vashishtha, Bishwajit Kundu and Monidipa Ghosh
    Citation: BMC Bioinformatics 2022 23:319
  16. Essential Proteins are demonstrated to exert vital functions on cellular processes and are indispensable for the survival and reproduction of the organism. Traditional centrality methods perform poorly on comp...

    Authors: Yi Yue, Chen Ye, Pei-Yun Peng, Hui-Xin Zhai, Iftikhar Ahmad, Chuan Xia, Yun-Zhi Wu and You-Hua Zhang
    Citation: BMC Bioinformatics 2022 23:318
  17. ImputAccur is a software tool to measure genotype-imputation accuracy. Imputation of untyped markers is a standard approach in genome-wide association studies to close the gap between directly genotyped and other...

    Authors: Kolja A. Thormann, Viola Tozzi, Paula Starke, Heike Bickeböller, Marcus Baum and Albert Rosenberger
    Citation: BMC Bioinformatics 2022 23:316
  18. Drug–target interaction (DTI) prediction plays a crucial role in drug discovery. Although the advanced deep learning has shown promising results in predicting DTIs, it still needs improvements in two aspects: ...

    Authors: Yuni Zeng, Xiangru Chen, Dezhong Peng, Lijun Zhang and Haixiao Huang
    Citation: BMC Bioinformatics 2022 23:314
  19. DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly ...

    Authors: Merlin Bardin, Pierre Rousselot-Pailley, Thierry Tron and Viviane Robert
    Citation: BMC Bioinformatics 2022 23:313
  20. Although there have been some recent cell and animal experiments indicating that expression of the gene encoding apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) is closely related to cancer, ...

    Authors: Jiacheng Wu, Ni Li, Linwen Zhu, Dawei Zhen, Mengqi Li, Hang Chen, Mengmeng Ye, Yiqin Wei and Guofeng Shao
    Citation: BMC Bioinformatics 2022 23:312
  21. Cervical cancer is the fourth most common cancer affecting women and is caused by human Papillomavirus (HPV) infections that are sexually transmitted. There are currently commercially available prophylactic va...

    Authors: Samira Sanami, Mahmoud Rafieian-Kopaei, Korosh Ashrafi Dehkordi, Hamidreza Pazoki-Toroudi, Fatemeh Azadegan-Dehkordi, Gholam-Reza Mobini, Morteza Alizadeh, Muhammad Sadeqi Nezhad, Maryam Ghasemi-Dehnoo and Nader Bagheri
    Citation: BMC Bioinformatics 2022 23:311
  22. Technical improvement in ATAC-seq makes it possible for high throughput profiling the chromatin states of single cells. However, data from multiple sources frequently show strong technical variations, which is...

    Authors: Li Lin and Liye Zhang
    Citation: BMC Bioinformatics 2022 23:309
  23. Heritability and genetic correlation can be estimated from genome-wide single-nucleotide polymorphism (SNP) data using various methods. We recently developed multivariate genomic-relatedness-based restricted m...

    Authors: Ronald De Vlaming, Eric A. W. Slob, Patrick J. F. Groenen and Cornelius A. Rietveld
    Citation: BMC Bioinformatics 2022 23:305
  24. Previous studies have demonstrated the value of re-analysing publicly available genetics data with recent analytical approaches. Publicly available datasets, such as the Women’s Health Initiative (WHI) offered...

    Authors: Adam N. Bennett, Jethro Rainford, Xiaotai Huang, Qian He and Kei Hang Katie Chan
    Citation: BMC Bioinformatics 2022 23:304
  25. The discovery of critical biomarkers is significant for clinical diagnosis, drug research and development. Researchers usually obtain biomarkers from microarray data, which comes from the dimensional curse. Fe...

    Authors: Weidong Xie, Wei Li, Shoujia Zhang, Linjie Wang, Jinzhu Yang and Dazhe Zhao
    Citation: BMC Bioinformatics 2022 23:303
  26. Probabilistic functional integrated networks (PFINs) are designed to aid our understanding of cellular biology and can be used to generate testable hypotheses about protein function. PFINs are generally create...

    Authors: Katherine James, Aoesha Alsobhe, Simon J Cockell, Anil Wipat and Matthew Pocock
    Citation: BMC Bioinformatics 2022 23:302
  27. Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic a...

    Authors: M. Walder, E. Edelstein, M. Carroll, S. Lazarev, J. E. Fajardo, A. Fiser and R. Viswanathan
    Citation: BMC Bioinformatics 2022 23:301
  28. Protein complexes are essential for biologists to understand cell organization and function effectively. In recent years, predicting complexes from protein–protein interaction (PPI) networks through computatio...

    Authors: Xiaoxu Wang, Yijia Zhang, Peixuan Zhou and Xiaoxia Liu
    Citation: BMC Bioinformatics 2022 23:300
  29. A large number of evidences from biological experiments have confirmed that miRNAs play an important role in the progression and development of various human complex diseases. However, the traditional experime...

    Authors: Dan Huang, JiYong An, Lei Zhang and BaiLong Liu
    Citation: BMC Bioinformatics 2022 23:299
  30. The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, identifying many cancer-associated genes. Although cancers in the same tissue are w...

    Authors: Amin Ghareyazi, Amirreza Kazemi, Kimia Hamidieh, Hamed Dashti, Maedeh Sadat Tahaei, Hamid R. Rabiee, Hamid Alinejad-Rokny and Iman Dehzangi
    Citation: BMC Bioinformatics 2022 23:298
  31. Mediation analysis plays a major role in identifying significant mediators in the pathway between environmental exposures and health outcomes. With advanced data collection technology for large-scale studies, ...

    Authors: Chamila Perera, Haixiang Zhang, Yinan Zheng, Lifang Hou, Annie Qu, Cheng Zheng, Ke Xie and Lei Liu
    Citation: BMC Bioinformatics 2022 23:296
  32. Computer-aided analysis of biological images typically requires extensive training on large-scale annotated datasets, which is not viable in many situations. In this paper, we present Generative Adversarial Ne...

    Authors: Alessio Mascolini, Dario Cardamone, Francesco Ponzio, Santa Di Cataldo and Elisa Ficarra
    Citation: BMC Bioinformatics 2022 23:295

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