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  1. Determining cell identity in volumetric images of tagged neuronal nuclei is an ongoing challenge in contemporary neuroscience. Frequently, cell identity is determined by aligning and matching tags to an “atlas...

    Authors: Michael Skuhersky, Tailin Wu, Eviatar Yemini, Amin Nejatbakhsh, Edward Boyden and Max Tegmark
    Citation: BMC Bioinformatics 2022 23:195
  2. Finding correlation patterns is an important goal of analyzing biological data. Currently available methods for correlation analysis mainly use non-direct associations, such as the Pearson correlation coeffici...

    Authors: Yi-Hua Jiang, Jie Long, Zhi-Bin Zhao, Liang Li, Zhe-Xiong Lian, Zhi Liang and Jia-Rui Wu
    Citation: BMC Bioinformatics 2022 23:194
  3. X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associa...

    Authors: Wen-Yi Yu, Yu Zhang, Meng-Kai Li, Zi-Ying Yang, Wing Kam Fung, Pei-Zhen Zhao and Ji-Yuan Zhou
    Citation: BMC Bioinformatics 2022 23:193
  4. The effectiveness of biclustering, simultaneous clustering of rows and columns in a data matrix, was shown in gene expression data analysis. Several researchers recognize its potentialities in other research a...

    Authors: Eduardo N. Castanho, Helena Aidos and Sara C. Madeira
    Citation: BMC Bioinformatics 2022 23:192
  5. Interpretation of high-throughput gene expression data continues to require mathematical tools in data analysis that recognizes the shape of the data in high dimensions. Topological data analysis (TDA) has rec...

    Authors: Tamal K. Dey, Sayan Mandal and Soham Mukherjee
    Citation: BMC Bioinformatics 2022 22(Suppl 10):627

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

  6. Gene expression is the result of the balance between transcription and degradation. Recent experimental findings have shown fine and specific regulation of RNA degradation and the presence of various molecular...

    Authors: Federica Conte, Federico Papa, Paola Paci and Lorenzo Farina
    Citation: BMC Bioinformatics 2022 23:190
  7. Nowadays, the inception of computer modeling and simulation in life science is a matter of fact. This is one of the reasons why regulatory authorities are open in considering in silico trials evidence for the ...

    Authors: Giulia Russo, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi and Francesco Pappalardo
    Citation: BMC Bioinformatics 2022 22(Suppl 14):626

    This article is part of a Supplement: Volume 22 Supplement 14

  8. Many long non-coding RNAs (lncRNAs) have key roles in different human biologic processes and are closely linked to numerous human diseases, according to cumulative evidence. Predicting potential lncRNA-disease...

    Authors: Ying Liang, Ze-Qun Zhang, Nian-Nian Liu, Ya-Nan Wu, Chang-Long Gu and Ying-Long Wang
    Citation: BMC Bioinformatics 2022 23:189
  9. Identifying associations among biological variables is a major challenge in modern quantitative biological research, particularly given the systemic and statistical noise endemic to biological systems. Drug se...

    Authors: Petr Smirnov, Ian Smith, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner and Benjamin Haibe-Kains
    Citation: BMC Bioinformatics 2022 23:188
  10. Using DNA as a storage medium is appealing due to the information density and longevity of DNA, especially in the era of data explosion. A significant challenge in the DNA data storage area is to deal with the...

    Authors: Lekang Yuan, Zhen Xie, Ye Wang and Xiaowo Wang
    Citation: BMC Bioinformatics 2022 23:185
  11. Stomach adenocarcinoma (STAD) is a common malignant tumor in the world and its prognosis is poor, miRNA plays a role mainly by influencing the expression of mRNAs, and participates in the occurrence and develo...

    Authors: Hao Qian, Nanxue Cui, Qiao Zhou and Shihai Zhang
    Citation: BMC Bioinformatics 2022 23:181
  12. The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMP...

    Authors: Reji Manjunathan, Vijayalakshmi Periyaswami, Kartik Mitra, Arokiaraj Sherlin Rosita, Medha Pandya, Jayaraman Selvaraj, Lokesh Ravi, Nalini Devarajan and Mukesh Doble
    Citation: BMC Bioinformatics 2022 23:180
  13. When analyzing large datasets from high-throughput technologies, researchers often encounter missing quantitative measurements, which are particularly frequent in metabolomics datasets. Metabolomics, the compr...

    Authors: Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh and Katerina Kechris
    Citation: BMC Bioinformatics 2022 23:179
  14. Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors–subsets of the state space towards which the BN...

    Authors: Nikola Beneš, Luboš Brim, Jakub Kadlecaj, Samuel Pastva and David Šafránek
    Citation: BMC Bioinformatics 2022 23:173
  15. Clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers are important components of prokaryotic CRISPR-Cas systems. In order to analyze the CRISPR loci of multiple genomes more int...

    Authors: Lei Sun, Jinbiao Wang, Fu Yan, Gongming Wang, Yun Li and Jinlin Huang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):172

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

  16. Archaea are a vast and unexplored domain. Bioinformatic techniques might enlighten the path to a higher quality genome annotation in varied organisms. Promoter sequences of archaea have the action of a plethor...

    Authors: Gustavo Sganzerla Martinez, Ernesto Pérez-Rueda, Sharmilee Sarkar, Aditya Kumar and Scheila de Ávila e Silva
    Citation: BMC Bioinformatics 2022 23:171
  17. Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarray...

    Authors: Junyao Kuang, Nicolas Buchon, Kristin Michel and Caterina Scoglio
    Citation: BMC Bioinformatics 2022 23:170
  18. De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structur...

    Authors: Riku Walve and Leena Salmela
    Citation: BMC Bioinformatics 2022 23:167
  19. To reduce drug side effects and enhance their therapeutic effect compared with single drugs, drug combination research, combining two or more drugs, is highly important. Conducting in-vivo and in-vitro experim...

    Authors: Yongsun Shim, Munhwan Lee, Pil-Jong Kim and Hong-Gee Kim
    Citation: BMC Bioinformatics 2022 23:163
  20. Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cu...

    Authors: Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin and Shaowen Li
    Citation: BMC Bioinformatics 2022 23:162
  21. 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

  22. 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
  23. 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
  24. 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

  25. 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
  26. 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
  27. 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
  28. 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

  29. 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
  30. 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

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