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  3. With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from...

    Authors: Jindan Guo, Erli Pang, Hongtao Song and Kui Lin

    Citation: BMC Bioinformatics 2021 22:282

    Content type: Methodology article

    Published on:

  4. Single-cell RNA sequencing (scRNA-seq) has emerged has a main strategy to study transcriptional activity at the cellular level. Clustering analysis is routinely performed on scRNA-seq data to explore, recogniz...

    Authors: Madalina Ciortan and Matthieu Defrance

    Citation: BMC Bioinformatics 2021 22:280

    Content type: Research

    Published on:

  5. With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation ...

    Authors: Swapna Vidhur Daulatabad, Rajneesh Srivastava and Sarath Chandra Janga

    Citation: BMC Bioinformatics 2021 22:279

    Content type: Database

    Published on:

  7. Small Proteins have received increasing attention in recent years. They have in particular been implicated as signals contributing to the coordination of bacterial communities. In genome annotations they are o...

    Authors: John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen and Peter F Stadler

    Citation: BMC Bioinformatics 2021 22:277

    Content type: Research

    Published on:

  9. Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregula...

    Authors: Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson and Stephanie D. Byrum

    Citation: BMC Bioinformatics 2021 22:275

    Content type: Software

    Published on:

  10. Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, usin...

    Authors: Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan and Willy Albert Flegel

    Citation: BMC Bioinformatics 2021 22:273

    Content type: Research

    Published on:

  11. Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provi...

    Authors: Gezheng Xu, Wenge Rong, Yanmeng Wang, Yuanxin Ouyang and Zhang Xiong

    Citation: BMC Bioinformatics 2021 22:272

    Content type: Research

    Published on:

  12. Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo...

    Authors: Wei-Sheng Wu, Yi-Hong Tsao, Sheng-Cian Shiue, Ting-Yu Chen, Yan-Yuan Tseng and Joseph T. Tseng

    Citation: BMC Bioinformatics 2021 22(Suppl 10):271

    Content type: Research

    Published on:

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

  13. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival rate. Despite microRNAs (miRNAs) are used as potential biomarkers in ma...

    Authors: Eskezeia Y. Dessie, Jeffrey J. P. Tsai, Jan-Gowth Chang and Ka-Lok Ng

    Citation: BMC Bioinformatics 2021 22(Suppl 10):270

    Content type: Methodology

    Published on:

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

  16. Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended descript...

    Authors: Gwenaëlle G. Lemoine, Marie-Pier Scott-Boyer, Bathilde Ambroise, Olivier Périn and Arnaud Droit

    Citation: BMC Bioinformatics 2021 22:267

    Content type: Research

    Published on:

  17. Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA...

    Authors: Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens and Gregory R. Grant

    Citation: BMC Bioinformatics 2021 22:266

    Content type: Review

    Published on:

  18. Testing for differential abundance of microbes in disease is a common practice in microbiome studies. Numerous differential abundance (DA) testing methods exist and range from traditional statistical tests to ...

    Authors: Zachary D. Wallen

    Citation: BMC Bioinformatics 2021 22:265

    Content type: Research article

    Published on:

  19. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Due to the technical challenges involv...

    Authors: Gilad Ben Or and Isana Veksler-Lublinsky

    Citation: BMC Bioinformatics 2021 22:264

    Content type: Research article

    Published on:

  22. Moonlighting proteins (MPs) are a subclass of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Identification of unknown cellular p...

    Authors: Farshid Shirafkan, Sajjad Gharaghani, Karim Rahimian, Reza Hasan Sajedi and Javad Zahiri

    Citation: BMC Bioinformatics 2021 22:261

    Content type: Research

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:366

  23. Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mous...

    Authors: David Borland, Carolyn M. McCormick, Niyanta K. Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim, Guorong Wu and Jason L. Stein

    Citation: BMC Bioinformatics 2021 22:260

    Content type: Software

    Published on:

  24. Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for sev...

    Authors: In-Hee Lee, Yufei Lin, William Jefferson Alvarez, Carles Hernandez-Ferrer, Kenneth D. Mandl and Sek Won Kong

    Citation: BMC Bioinformatics 2021 22:259

    Content type: Software

    Published on:

  27. Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcodi...

    Authors: T. M. Porter and M. Hajibabaei

    Citation: BMC Bioinformatics 2021 22:256

    Content type: Methodology article

    Published on:

  28. With the development of the technology of single-cell sequence, revealing homogeneity and heterogeneity between cells has become a new area of computational systems biology research. However, the clustering of...

    Authors: Yuanyuan Li, Ping Luo, Yi Lu and Fang-Xiang Wu

    Citation: BMC Bioinformatics 2021 22(Suppl 3):255

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  29. Colocalization is a statistical method used in genetics to determine whether the same variant is causal for multiple phenotypes, for example, complex traits and gene expression. It provides stronger mechanisti...

    Authors: Emily A. King, Fengjiao Dunbar, Justin Wade Davis and Jacob F. Degner

    Citation: BMC Bioinformatics 2021 22:254

    Content type: Methodology article

    Published on:

  30. DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein–DNA interfaces. As experimental methods for identifying...

    Authors: Sijia Zhang, Lihua Wang, Le Zhao, Menglu Li, Mengya Liu, Ke Li, Yannan Bin and Junfeng Xia

    Citation: BMC Bioinformatics 2021 22(Suppl 3):253

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  31. Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensit...

    Authors: Alexander Partin, Thomas Brettin, Yvonne A. Evrard, Yitan Zhu, Hyunseung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow and Rick L. Stevens

    Citation: BMC Bioinformatics 2021 22:252

    Content type: Research article

    Published on:

  35. Some proposed methods for identifying essential proteins have better results by using biological information. Gene expression data is generally used to identify essential proteins. However, gene expression dat...

    Authors: Jiancheng Zhong, Chao Tang, Wei Peng, Minzhu Xie, Yusui Sun, Qiang Tang, Qiu Xiao and Jiahong Yang

    Citation: BMC Bioinformatics 2021 22:248

    Content type: Research article

    Published on:

  36. Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SA...

    Authors: Sanket Desai, Aishwarya Rane, Asim Joshi and Amit Dutt

    Citation: BMC Bioinformatics 2021 22:247

    Content type: Software

    Published on:

  39. The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era ...

    Authors: Junyi Li, Huinian Li, Xiao Ye, Li Zhang, Qingzhe Xu, Yuan Ping, Xiaozhu Jing, Wei Jiang, Qing Liao, Bo Liu and Yadong Wang

    Citation: BMC Bioinformatics 2021 22(Suppl 3):243

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  40. The state-of-the-art deep learning based cancer type prediction can only predict cancer types whose samples are available during the training where the sample size is commonly large. In this paper, we consider...

    Authors: Milad Mostavi, Yu-Chiao Chiu, Yidong Chen and Yufei Huang

    Citation: BMC Bioinformatics 2021 22:244

    Content type: Research article

    Published on:

  41. Long noncoding RNAs (lncRNAs) play an important role in regulating biological activities and their prediction is significant for exploring biological processes. Long short-term memory (LSTM) and convolutional ...

    Authors: Jun Meng, Qiang Kang, Zheng Chang and Yushi Luan

    Citation: BMC Bioinformatics 2021 22(Suppl 3):242

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  42. In the development of science and technology, there are increasing evidences that there are some associations between lncRNAs and human diseases. Therefore, finding these associations between them will have a ...

    Authors: Jin-Xing Liu, Ming-Ming Gao, Zhen Cui, Ying-Lian Gao and Feng Li

    Citation: BMC Bioinformatics 2021 22(Suppl 3):241

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  44. Current methods in machine learning provide approaches for solving challenging, multiple constraint design problems. While deep learning and related neural networking methods have state-of-the-art performance,...

    Authors: Kyle Boone, Cate Wisdom, Kyle Camarda, Paulette Spencer and Candan Tamerler

    Citation: BMC Bioinformatics 2021 22:239

    Content type: Research article

    Published on:

  47. High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic refere...

    Authors: Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange and Gerhard Schöfl

    Citation: BMC Bioinformatics 2021 22:236

    Content type: Software

    Published on:

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