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  2. Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, ana...

    Authors: Xuemin Dong, Shanshan Dong, Shengkai Pan and Xiangjiang Zhan
    Citation: BMC Bioinformatics 2022 23:26
    Content type: Software Published on:

  3. Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parame...

    Authors: Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik and Somali Chaterji
    Citation: BMC Bioinformatics 2022 23:25
    Content type: Methodology article Published on:

  5. Ontology-based semantic similarity measures based on SNOMED-CT, MeSH, and Gene Ontology are being extensively used in many applications in biomedical text mining and genomics respectively, which has encouraged...

    Authors: Juan J. Lastra-Díaz, Alicia Lara-Clares and Ana Garcia-Serrano
    Citation: BMC Bioinformatics 2022 23:23
    Content type: Software Published on:

  6. As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also to develop better treatment strategies using existing drugs to ...

    Authors: Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen and Pia Abel zur Wiesch
    Citation: BMC Bioinformatics 2022 23:22
    Content type: Software Published on:

  7. Next-generation sequencing (NGS) is nowadays the most used high-throughput technology for DNA sequencing. Among others NGS enables the in-depth analysis of immune repertoires. Research in the field of T cell r...

    Authors: Julia Vetter, Susanne Schaller, Andreas Heinzel, Constantin Aschauer, Roman Reindl-Schwaighofer, Kira Jelencsics, Karin Hu, Rainer Oberbauer and Stephan M. Winkler
    Citation: BMC Bioinformatics 2022 23:21
    Content type: Software Published on:

  10. The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, mod...

    Authors: Jörg Winkler, Gianvito Urgese, Elisa Ficarra and Knut Reinert
    Citation: BMC Bioinformatics 2022 23:18
    Content type: Software Published on:

  11. A limitation of traditional differential expression analysis on small datasets involves the possibility of false positives and false negatives due to sample variation. Considering the recent advances in deep l...

    Authors: Tulika Kakati, Dhruba K. Bhattacharyya, Jugal K. Kalita and Trina M. Norden-Krichmar
    Citation: BMC Bioinformatics 2022 23:17
    Content type: Methodology article Published on:

  12. Single-cell RNA sequencing is becoming a powerful tool to identify cell states, reconstruct developmental trajectories, and deconvolute spatial expression. The rapid development of computational methods promot...

    Authors: Huijian Feng, Lihui Lin and Jiekai Chen
    Citation: BMC Bioinformatics 2022 23:16
    Content type: Software Published on:

  13. RIFINs and STEVORs are variant surface antigens expressed by P. falciparum that play roles in severe malaria pathogenesis and immune evasion. These two highly diverse multigene families feature multiple paralogs,...

    Authors: Albert E. Zhou, Zalak V. Shah, Katie R. Bradwell, James B. Munro, Andrea A. Berry, David Serre, Shannon Takala-Harrison, Timothy D. O’Connor, Joana C. Silva and Mark A. Travassos
    Citation: BMC Bioinformatics 2022 23:15
    Content type: Software Published on:

  15. The temporal progression of many fundamental processes in cells and organisms, including homeostasis, differentiation and development, are governed by gene regulatory networks (GRNs). GRNs balance fluctuations...

    Authors: Johannes Hettich and J. Christof M. Gebhardt
    Citation: BMC Bioinformatics 2022 23:13
    Content type: Research Published on:

  16. Construction of networks from cross-sectional biological data is increasingly common. Many recent methods have been based on Gaussian graphical modeling, and prioritize estimation of conditional pairwise depen...

    Authors: Nathan P. Gill, Raji Balasubramanian, James R. Bain, Michael J. Muehlbauer, William L. Lowe Jr. and Denise M. Scholtens
    Citation: BMC Bioinformatics 2022 23:12
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2022 23:462

  18. Dietary restriction (DR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identifi...

    Authors: Gustavo Daniel Vega Magdaleno, Vladislav Bespalov, Yalin Zheng, Alex A. Freitas and Joao Pedro de Magalhaes
    Citation: BMC Bioinformatics 2022 23:10
    Content type: Research Published on:

  23. More and more evidence showed that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human sophisticated diseases. Therefore, predicting human lncRNA-disease association...

    Authors: Liugen Wang, Min Shang, Qi Dai and Ping-an He
    Citation: BMC Bioinformatics 2022 23:5
    Content type: Research Published on:

  24. Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through po...

    Authors: Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis and Karin Verspoor
    Citation: BMC Bioinformatics 2022 23:4
    Content type: Research Published on:

  26. Cellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific exp...

    Authors: Shaoheng Liang, Jason Willis, Jinzhuang Dou, Vakul Mohanty, Yuefan Huang, Eduardo Vilar and Ken Chen
    Citation: BMC Bioinformatics 2022 23:2
    Content type: Research Published on:

  27. Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable s...

    Authors: Brandon C Reyes, Irene Otero-Muras and Vladislav A Petyuk
    Citation: BMC Bioinformatics 2022 23:1
    Content type: Research Published on:

  29. Exogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. I...

    Authors: Meifang Qi, Utthara Nayar, Leif S. Ludwig, Nikhil Wagle and Esther Rheinbay
    Citation: BMC Bioinformatics 2021 22:611
    Content type: Software Published on:

  33. Genome-wide association studies have identified thousands of genetic susceptibility loci associated with cancer as well as other traits and diseases. Mapping germline variation in identified genetic susceptibi...

    Authors: Shu-Hong Lin, Rohit Thakur and Mitchell J. Machiela
    Citation: BMC Bioinformatics 2021 22:608
    Content type: Database Published on:

  34. Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the incre...

    Authors: João Victor da Silva Guerra, Helder Veras Ribeiro-Filho, Gabriel Ernesto Jara, Leandro Oliveira Bortot, José Geraldo de Carvalho Pereira and Paulo Sérgio Lopes-de-Oliveira
    Citation: BMC Bioinformatics 2021 22:607
    Content type: Software Published on:

  36. Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional cha...

    Authors: Federico Martinez-Seidel, Yin-Chen Hsieh, Dirk Walther, Joachim Kopka and Alexandre Augusto Pereira Firmino
    Citation: BMC Bioinformatics 2021 22:605
    Content type: Software Published on:

  37. In population genomics, polymorphisms that are highly differentiated between geographically separated populations are often suggestive of Darwinian positive selection. Genomic scans have highlighted several su...

    Authors: Fadilla Wahyudi, Farhang Aghakhanian, Sadequr Rahman, Yik-Ying Teo, Michał Szpak, Jasbir Dhaliwal and Qasim Ayub
    Citation: BMC Bioinformatics 2021 22:604
    Content type: Software Published on:

  39. The recognition of pharmacological substances, compounds and proteins is essential for biomedical relation extraction, knowledge graph construction, drug discovery, as well as medical question answering. Altho...

    Authors: Cong Sun, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang
    Citation: BMC Bioinformatics 2021 22(Suppl 1):602
    Content type: Research Published on:

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

  40. The volume of biomedical literature and clinical data is growing at an exponential rate. Therefore, efficient access to data described in unstructured biomedical texts is a crucial task for the biomedical indu...

    Authors: Renzo M. Rivera-Zavala and Paloma Martínez
    Citation: BMC Bioinformatics 2021 22(Suppl 1):601
    Content type: Research Published on:

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

  41. Biomedical named entity recognition (NER) is a fundamental task of biomedical text mining that finds the boundaries of entity mentions in biomedical text and determines their entity type. To accelerate the dev...

    Authors: Ying Xiong, Shuai Chen, Buzhou Tang, Qingcai Chen, Xiaolong Wang, Jun Yan and Yi Zhou
    Citation: BMC Bioinformatics 2021 22(Suppl 1):600
    Content type: Research Published on:

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

  42. Natural language processing (NLP) and text mining technologies for the extraction and indexing of chemical and drug entities are key to improving the access and integration of information from unstructured dat...

    Authors: Pilar López-Úbeda, Manuel Carlos Díaz-Galiano, L. Alfonso Ureña-López and M. Teresa Martín-Valdivia
    Citation: BMC Bioinformatics 2021 22(Suppl 1):599
    Content type: Research Published on:

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

  43. Automated assignment of specific ontology concepts to mentions in text is a critical task in biomedical natural language processing, and the subject of many open shared tasks. Although the current state of the...

    Authors: Mayla R. Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr. and Lawrence E. Hunter
    Citation: BMC Bioinformatics 2021 22(Suppl 1):598
    Content type: Research Published on:

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

  44. At present, the bioinformatics research on the relationship between aging-related diseases and genes is mainly through the establishment of a machine learning multi-label model to classify each gene. Most of t...

    Authors: Junhua Ye, Shunfang Wang, Xin Yang and Xianjun Tang
    Citation: BMC Bioinformatics 2021 22:597
    Content type: Research Published on:

  45. Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationsh...

    Authors: William F. Anjos, Gabriel C. Lanes, Vasco A. Azevedo and Anderson R. Santos
    Citation: BMC Bioinformatics 2021 22:596
    Content type: Software Published on:

  46. Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. ...

    Authors: Nanette Christie, Chanaka Mannapperuma, Raphael Ployet, Karen van der Merwe, Niklas Mähler, Nicolas Delhomme, Sanushka Naidoo, Eshchar Mizrachi, Nathaniel R. Street and Alexander A. Myburg
    Citation: BMC Bioinformatics 2021 22:595
    Content type: Database Published on:

  47. Supervised classification methods have been used for many years for feature selection in metabolomics and other omics studies. We developed a novel primal-dual based classification method (PD-CR) that can perf...

    Authors: David Chardin, Olivier Humbert, Caroline Bailleux, Fanny Burel-Vandenbos, Valerie Rigau, Thierry Pourcher and Michel Barlaud
    Citation: BMC Bioinformatics 2021 22:594
    Content type: Research Published on:

  48. In bacteria, genes with related functions—such as those involved in the metabolism of the same compound or in infection processes—are often physically close on the genome and form groups called clusters. The e...

    Authors: Chiara E. Cotroneo, Isobel Claire Gormley, Denis C. Shields and Michael Salter-Townshend
    Citation: BMC Bioinformatics 2021 22:593
    Content type: Research Published on:

  49. Next-generation sequencing platforms allow us to sequence millions of small fragments of DNA simultaneously, revolutionizing cancer research. Sequence analysis has revealed that cancer driver genes operate acr...

    Authors: Ying Hu, Chunhua Yan, Qingrong Chen and Daoud Meerzaman
    Citation: BMC Bioinformatics 2021 22:592
    Content type: Software Published on:

  50. Clinical notes are documents that contain detailed information about the health status of patients. Medical codes generally accompany them. However, the manual diagnosis is costly and error-prone. Moreover, la...

    Authors: Xingwang Li, Yijia Zhang, Faiz ul Islam, Deshi Dong, Hao Wei and Mingyu Lu
    Citation: BMC Bioinformatics 2021 22:590
    Content type: Research Published on:

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