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  1. Drug discovery is time-consuming and costly. Machine learning, especially deep learning, shows great potential in quantitative structure–activity relationship (QSAR) modeling to accelerate drug discovery proce...

    Authors: Yang Liu, Hansaim Lim and Lei Xie
    Citation: BMC Bioinformatics 2022 23(Suppl 3):158

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

  2. Although single-cell RNA sequencing of xenograft samples has been widely used, no comprehensive bioinformatics pipeline is available for human and mouse mixed single-cell analyses. Considering the numerous hom...

    Authors: Jaeyong Choi, Woochan Lee, Jung-Ki Yoon, Sun Mi Choi, Chang-Hoon Lee, Hyeong-Gon Moon, Sukki Cho, Jin-Haeng Chung, Han-Kwang Yang and Jong-Il Kim
    Citation: BMC Bioinformatics 2022 23:157
  3. Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq ex...

    Authors: John A. Hadish, Tyler D. Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman B. McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren Honaas and Stephen P. Ficklin
    Citation: BMC Bioinformatics 2022 23:156
  4. As many complex omics data have been generated during the last two decades, dimensionality reduction problem has been a challenging issue in better mining such data. The omics data typically consists of many f...

    Authors: Tapas Bhadra, Saurav Mallik, Neaj Hasan and Zhongming Zhao
    Citation: BMC Bioinformatics 2022 23(Suppl 3):153

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

  5. T cell receptors (TCRs) play critical roles in adaptive immune responses, and recent advances in genome technology have made it possible to examine the T cell receptor (TCR) repertoire at the individual sequen...

    Authors: Meiling Liu, Juna Goo, Yang Liu, Wei Sun, Michael C. Wu, Li Hsu and Qianchuan He
    Citation: BMC Bioinformatics 2022 23:152
  6. Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with ...

    Authors: Fabrizio Frasca, Matteo Matteucci, Michele Leone, Marco J. Morelli and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:151
  7. Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to...

    Authors: Kyle Fletcher, Rongkui Han, Diederik Smilde and Richard Michelmore
    Citation: BMC Bioinformatics 2022 23:150
  8. The widely spreading coronavirus disease (COVID-19) has three major spreading properties: pathogenic mutations, spatial, and temporal propagation patterns. We know the spread of the virus geographically and te...

    Authors: Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin and Sun Kim
    Citation: BMC Bioinformatics 2022 23(Suppl 3):149

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

  9. SNARE proteins play an important role in different biological functions. This study aims to investigate the contribution of a new class of molecular descriptors (called SNARER) related to the chemical-physical...

    Authors: Alessia Auriemma Citarella, Luigi Di Biasi, Michele Risi and Genoveffa Tortora
    Citation: BMC Bioinformatics 2022 23:148
  10. Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted and are now turning to single cell measureme...

    Authors: Micha Hersch, Adriano Biasini, Ana C. Marques and Sven Bergmann
    Citation: BMC Bioinformatics 2022 23:147
  11. 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
  12. ‘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
  13. 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

  14. 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

  15. 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

  16. 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

  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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

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