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  1. Autism spectrum disorder (ASD) is a group of complex neurodevelopment disorders with a strong genetic basis. Large scale sequencing studies have identified over one hundred ASD risk genes. Nevertheless, the va...

    Authors: Ying Ji, Rui Chen, Quan Wang, Qiang Wei, Ran Tao and Bingshan Li
    Citation: BMC Bioinformatics 2022 23:146
  2. ‘De novo’ drug discovery is costly, slow, and with high risk. Repurposing known drugs for treatment of other diseases offers a fast, low-cost/risk and highly-efficient method toward development of efficacious tre...

    Authors: Forough Firoozbakht, Iman Rezaeian, Luis Rueda and Alioune Ngom
    Citation: BMC Bioinformatics 2022 23:143
  3. Being able to efficiently call variants from the increasing amount of sequencing data daily produced from multiple viral strains is of the utmost importance, as demonstrated during the COVID-19 pandemic, in or...

    Authors: Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola and Marco Previtali
    Citation: BMC Bioinformatics 2022 22(Suppl 15):625

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

  4. The gene signatures have been considered as a promising early diagnosis and prognostic analysis to identify disease subtypes and to determine subsequent treatments. Tissue-specific gene signatures of a specifi...

    Authors: Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yi-Hsuan Chuang, Jung-Yu Lee and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2022 22(Suppl 10):624

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

  5. Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure feat...

    Authors: Xiao Chen and Jianlin Cheng
    Citation: BMC Bioinformatics 2022 23(Suppl 3):141

    This article is part of a Supplement: Volume 23 Supplement 3

  6. Chronic cough affects approximately 10% of adults. The lack of ICD codes for chronic cough makes it challenging to apply supervised learning methods to predict the characteristics of chronic cough patients, th...

    Authors: Wei Shao, Xiao Luo, Zuoyi Zhang, Zhi Han, Vasu Chandrasekaran, Vladimir Turzhitsky, Vishal Bali, Anna R. Roberts, Megan Metzger, Jarod Baker, Carmen La Rosa, Jessica Weaver, Paul Dexter and Kun Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):140

    This article is part of a Supplement: Volume 23 Supplement 3

  7. With a growing amount of (multi-)omics data being available, the extraction of knowledge from these datasets is still a difficult problem. Classical enrichment-style analyses require predefined pathways or gen...

    Authors: Sebastian Winkler, Ivana Winkler, Mirjam Figaschewski, Thorsten Tiede, Alfred Nordheim and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2022 23:139
  8. Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Recent studies have observed causative mutations in susceptible genes related to colorectal cancer in 10 to 15% of the p...

    Authors: Hamed Dashti, Iman Dehzangi, Masroor Bayati, James Breen, Amin Beheshti, Nigel Lovell, Hamid R. Rabiee and Hamid Alinejad-Rokny
    Citation: BMC Bioinformatics 2022 23:138
  9. SARS-CoV-2 virus sequencing has been applied to track the COVID-19 pandemic spread and assist the development of PCR-based diagnostics, serological assays, and vaccines. With sequencing becoming routine global...

    Authors: Jody Phelan, Wouter Deelder, Daniel Ward, Susana Campino, Martin L. Hibberd and Taane G. Clark
    Citation: BMC Bioinformatics 2022 23:137
  10. Medical information has rapidly increased on the internet and has become one of the main targets of search engine use. However, medical information on the internet is subject to the problems of quality and acc...

    Authors: Li Zhang, Xiaoran Yang, Shijian Li, Tianyi Liao and Gang Pan
    Citation: BMC Bioinformatics 2022 23:136
  11. Long non-coding RNA (LncRNA) plays important roles in physiological and pathological processes. Identifying LncRNA–protein interactions (LPIs) is essential to understand the molecular mechanism and infer the f...

    Authors: Ying Li, Lizheng Wei, Cankun Wang, Jianing Zhao, Siyu Han, Yu Zhang and Wei Du
    Citation: BMC Bioinformatics 2022 23:135
  12. Retroviruses replicate by integrating a DNA copy into a host chromosome. Detecting novel retroviral integrations (ones not in the reference genome sequence of the host) from genomic NGS data is bioinformatical...

    Authors: Emanuele Marchi, Mathew Jones, Paul Klenerman, John Frater, Gkikas Magiorkinis and Robert Belshaw
    Citation: BMC Bioinformatics 2022 23:134
  13. Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrolla...

    Authors: Paolo Inglese, Helen Xuexia Huang, Vincen Wu, Matthew R. Lewis and Zoltan Takats
    Citation: BMC Bioinformatics 2022 23:133
  14. Converting molecules into computer-interpretable features with rich molecular information is a core problem of data-driven machine learning applications in chemical and drug-related tasks. Generally speaking, ...

    Authors: Hamid Hadipour, Chengyou Liu, Rebecca Davis, Silvia T. Cardona and Pingzhao Hu
    Citation: BMC Bioinformatics 2022 23(Suppl 4):132

    This article is part of a Supplement: Volume 23 Supplement 4

  15. Predicting which pathogens might exhibit antimicrobial resistance (AMR) based on genomics data is one of the promising ways to swiftly and precisely identify AMR pathogens. Currently, the most widely used geno...

    Authors: Ming-Ren Yang and Yu-Wei Wu
    Citation: BMC Bioinformatics 2022 23(Suppl 4):131

    This article is part of a Supplement: Volume 23 Supplement 4

  16. Human protein kinases play important roles in cancers, are highly co-regulated by kinase families rather than a single kinase, and complementarily regulate signaling pathways. Even though there are > 100,000 p...

    Authors: Yu-Wei Huang, Yen-Chao Hsu, Yi-Hsuan Chuang, Yun-Ti Chen, Xiang-Yu Lin, You-Wei Fan, Nikhil Pathak and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2022 23(Suppl 4):130

    This article is part of a Supplement: Volume 23 Supplement 4

  17. Drug resistance is a critical obstacle in cancer therapy. Discovering cancer drug response is important to improve anti-cancer drug treatment and guide anti-cancer drug design. Abundant genomic and drug respon...

    Authors: Tianxing Ma, Qiao Liu, Haochen Li, Mu Zhou, Rui Jiang and Xuegong Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 4):129

    This article is part of a Supplement: Volume 23 Supplement 4

  18. With the development of noninvasive imaging technology, collecting different imaging measurements of the same brain has become more and more easy. These multimodal imaging data carry complementary information ...

    Authors: Jin Zhang, Huiai Wang, Ying Zhao, Lei Guo and Lei Du
    Citation: BMC Bioinformatics 2022 23(Suppl 3):128

    This article is part of a Supplement: Volume 23 Supplement 3

  19. In research on new drug discovery, the traditional wet experiment has a long period. Predicting drug–target interaction (DTI) in silico can greatly narrow the scope of search of candidate medications. Excellen...

    Authors: Liyi Yu, Wangren Qiu, Weizhong Lin, Xiang Cheng, Xuan Xiao and Jiexia Dai
    Citation: BMC Bioinformatics 2022 23:126
  20. Immune microenvironment was closely related to the occurrence and progression of colorectal cancer (CRC). The objective of the current research was to develop and verify a Machine learning survival predictive ...

    Authors: Zhiqiao Zhang, Liwen Huang, Jing Li and Peng Wang
    Citation: BMC Bioinformatics 2022 23:124
  21. Heterogeneous omics data, increasingly collected through high-throughput technologies, can contain hidden answers to very important and still unsolved biomedical questions. Their integration and processing are...

    Authors: Simone Pallotta, Silvia Cascianelli and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:123
  22. The assembly task is an indispensable step in sequencing genomes of new organisms and studying structural genomic changes. In recent years, the dynamic development of next-generation sequencing (NGS) methods r...

    Authors: Katarzyna Nałęcz-Charkiewicz and Robert M. Nowak
    Citation: BMC Bioinformatics 2022 23:122
  23. As many interactions between the chemical and genomic space remain undiscovered, computational methods able to identify potential drug-target interactions (DTIs) are employed to accelerate drug discovery and r...

    Authors: E. Amiri Souri, R. Laddach, S. N. Karagiannis, L. G. Papageorgiou and S. Tsoka
    Citation: BMC Bioinformatics 2022 23:121
  24. Deep learning has become a prevalent method in identifying genomic regulatory sequences such as promoters. In a number of recent papers, the performance of deep learning models has continually been reported as...

    Authors: Raul I. Perez Martell, Alison Ziesel, Hosna Jabbari and Ulrike Stege
    Citation: BMC Bioinformatics 2022 23:118
  25. Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under activ...

    Authors: Borja González-Seoane, Christian Ponte-Fernández, Jorge González-Domínguez and María J. Martín
    Citation: BMC Bioinformatics 2022 23:117
  26. Understanding the role of various factors in 3D genome organization is essential to determine their impact on shaping large-scale chromatin units such as euchromatin (A) and heterochromatin (B) compartments. A...

    Authors: Mikhail D. Magnitov, Azat K. Garaev, Alexander V. Tyakht, Sergey V. Ulianov and Sergey V. Razin
    Citation: BMC Bioinformatics 2022 23:116
  27. Transcriptionally informed predictions are increasingly important for sub-typing cancer patients, understanding underlying biology and to inform novel treatment strategies. For instance, colorectal cancers (CR...

    Authors: Gerard P. Quinn, Tamas Sessler, Baharak Ahmaderaghi, Shauna Lambe, Harper VanSteenhouse, Mark Lawler, Mark Wappett, Bruce Seligmann, Daniel B. Longley and Simon S. McDade
    Citation: BMC Bioinformatics 2022 23:114
  28. Microalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae...

    Authors: Ana B. Romero-Losada, Christina Arvanitidou, Pedro de los Reyes, Mercedes García-González and Francisco J. Romero-Campero
    Citation: BMC Bioinformatics 2022 23:113
  29. Delivering tools for genome analysis to users is often difficult given the complex dependencies and conflicts of such tools. Container virtualization systems (such as Singularity) isolate environments, thereby...

    Authors: Xu Yang and Masahiro Kasahara
    Citation: BMC Bioinformatics 2022 23:112
  30. Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying imp...

    Authors: Josip Rudar, Teresita M. Porter, Michael Wright, G. Brian Golding and Mehrdad Hajibabaei
    Citation: BMC Bioinformatics 2022 23:110
  31. Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are...

    Authors: Elliott Swanson, Julian Reading, Lucas T. Graybuck and Peter J. Skene
    Citation: BMC Bioinformatics 2022 23:106
  32. Necrotizing enterocolitis (NEC) is a common, potentially catastrophic intestinal disease among very low birthweight premature infants. Affecting up to 15% of neonates born weighing less than 1500 g, NEC causes...

    Authors: Yun Chao Lin, Ansaf Salleb-Aouissi and Thomas A. Hooven
    Citation: BMC Bioinformatics 2022 23:104
  33. Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial wa...

    Authors: Lenz Furrer, Joseph Cornelius and Fabio Rinaldi
    Citation: BMC Bioinformatics 2022 22(Suppl 1):623

    This article is part of a Supplement: Volume 22 Supplement 1

  34. Just Another Gibbs Sampling (JAGS) is a convenient tool to draw posterior samples using Markov Chain Monte Carlo for Bayesian modeling. However, the built-in function dinterval() for censored data misspecifies th...

    Authors: Xinyue Qi, Shouhao Zhou and Martyn Plummer
    Citation: BMC Bioinformatics 2022 23:102
  35. lncRNAs play a critical role in numerous biological processes and life activities, especially diseases. Considering that traditional wet experiments for identifying uncovered lncRNA-disease associations is lim...

    Authors: Zhen-Hao Guo, Zhan-Heng Chen, Zhu-Hong You, Yan-Bin Wang, Hai-Cheng Yi and Mei-Neng Wang
    Citation: BMC Bioinformatics 2022 22(Suppl 5):622

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

  36. The prediction of protein secondary structures is a crucial and significant step for ab initio tertiary structure prediction which delivers the information about proteins activity and functions. As the experim...

    Authors: Katarzyna Stapor, Krzysztof Kotowski, Tomasz Smolarczyk and Irena Roterman
    Citation: BMC Bioinformatics 2022 23:100
  37. Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are intero...

    Authors: Malcolm E. Fisher, Erik Segerdell, Nicolas Matentzoglu, Mardi J. Nenni, Joshua D. Fortriede, Stanley Chu, Troy J. Pells, David Osumi-Sutherland, Praneet Chaturvedi, Christina James-Zorn, Nivitha Sundararaj, Vaneet S. Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov…
    Citation: BMC Bioinformatics 2022 23:99

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