Article
Biochemical Research Methods
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
Summary: With the rise in genomic data from sequencing technologies, the functions of many gene products remain unknown. High-throughput experiments are being conducted to address this gap, but the resulting annotations are biased towards less informative Gene Ontology terms. GOThresher, a Python tool, is introduced to identify and remove biases in protein function annotation databases, which is crucial for accurate understanding of protein function and training unbiased machine learning methods.
Article
Biochemical Research Methods
Alejandro A. Edera, Diego H. Milone, Georgina Stegmayer
Summary: A novel protocol anc2vec based on neural networks is proposed for constructing vector representations of GO terms, preserving ontological features and showing better performance on diverse tasks.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Computer Science, Software Engineering
T. Harbig, M. Witte Paz, K. Nieselt
Summary: Analysis pipelines in genomics, transcriptomics, and proteomics often produce lists of genes that overlap only partially or not at all and are too large for manual comparison. This paper presents GO-Compass, a visual analytics tool that reduces the redundancy and improves interpretability of gene lists by using semantic similarity. GO-Compass offers interactive visualizations, such as hierarchical clustering, treemaps, heatmaps, and bar charts, to facilitate the comparison of GO terms and gene information.
COMPUTER GRAPHICS FORUM
(2023)
Article
Biochemical Research Methods
Yang Li, Wang Keqi, Guohua Wang
Summary: The article introduces a novel approach to compute disease similarity by integrating disease-related genes and gene ontology hierarchy to learn disease representation based on deep representation learning. In the experiments, the AUC value of this method is 0.8074, improving the most competitive baseline method by 10.1%.
Article
Biochemical Research Methods
Xiaoshuai Zhang, Lixin Wang, Hucheng Liu, Xiaofeng Zhang, Bo Liu, Yadong Wang, Junyi Li
Summary: Protein is essential in living organisms and understanding its function is crucial for drug discovery and disease treatment. In this article, the authors propose the Prot2GO model, which integrates protein sequence and PPI network data to predict protein functions. The model achieves state-of-the-art performance on multiple metrics.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yi Chen, Fons. J. Verbeek, Katherine Wolstencroft
Summary: This study compares different strategies for mapping cancer hallmarks based on Gene Ontology and biological pathway annotation. The analysis of semantic similarity between annotations and gene set overlap reveals emerging consensus knowledge. The results highlight the importance of reaching a consensus in identifying cancer hallmark activity for systematic data integration and comparison between studies.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Yuanyuan Zhang, Ziqi Wang, Shudong Wang, Junliang Shang
Summary: The study systematically analyzes the performance of the GO graph and GOA graph in calculating the similarity of proteins using different graph embedding methods. It shows that graph embedding methods have advantages over traditional IC-based methods in calculating protein similarity, especially random walk graph embedding methods. Comparing link prediction experiment results from GO(DTW) and GOA(cosine) methods, it is shown that GO(DTW) features provide highly effective information for analyzing protein similarity.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Kaumadi L. Wijesooriya, Sameer Jadaan, Kaushalya L. Perera, Tanuveer Kaur, Mark L. Ziemann
Summary: The study revealed that the majority of functional enrichment studies in computational biology suffer from various issues such as inappropriate background gene lists, lack of statistical correction, and insufficient methodological details. This highlights the necessity for stronger standards in enrichment analysis to ensure the reliability of research results.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Computer Science, Information Systems
Samia Zouaoui, Khaled Rezeg
Summary: This paper proposes a novel approach called Multi-agents Indexing System to address plagiarism in Arabic documents. The system consists of three phases: natural language processing, indexing, and evaluation. The results show that the proposed system improves the performance of plagiarism detection in Arabic documents with semantic indexing and multi-agents system.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2022)
Article
Engineering, Electrical & Electronic
Zhao Lingling, Wang Junjie, Wang Chunyu, Guo Maozu
Summary: This article presents a new method for cross-domain semantic representation of biological ontologies based on natural language processing (NLP) and the BERT model. It demonstrates the ability of the method in analyzing and comparing biomedical entities in ontologies through word-level vector representations. The experimental results validate the effectiveness of the proposed method.
CHINESE JOURNAL OF ELECTRONICS
(2022)
Article
Biology
Luke T. Slater, Andreas Karwath, John A. Williams, Sophie Russell, Silver Makepeace, Alexander Carberry, Robert Hoehndorf, Georgios Gkoutos
Summary: This study developed a method to extract patient phenotype profiles from clinical narrative text and used semantic similarity to classify primary patient diagnosis. The results showed that uncurated text phenotypes can be a powerful tool for the differential diagnosis of common diseases.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Oncology
Jujuan Zhuang, Changjing Ren, Dan Ren, Yu'ang Li, Danyang Liu, Lingyu Cui, Geng Tian, Jiasheng Yang, Jingbo Liu
Summary: The study introduces a feature extraction method called FEGFS for analyzing scRNA-seq data based on known gene functions, outperforming other methods on small datasets. Additionally, CMF-Impute demonstrates strong capabilities in inferring cell lineage trajectories, and the clustering methods successfully identify important cell clusters related to glioma.
FRONTIERS IN ONCOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Goncalo Amaro, Filipe Moutinho, Rogerio Campos-Rebelo, Julius Kopke, Pedro Malo
Summary: This paper addresses data interchange format and interoperability issues between XML-based and JSON-based systems, proposing annotation mechanisms and translation algorithms to support interoperability between the two types of systems. The implementation of these algorithms in a prototype tool enables semantic compatibility verification and automatic generation of translators for system interoperability.
APPLIED SCIENCES-BASEL
(2021)
Article
Biochemical Research Methods
Ahmad Pesaranghader, Stan Matwin, Marina Sokolova, Jean-Christophe Grenier, Robert G. Beiko, Julie Hussin
Summary: This article introduces a deep learning method called deepSimDEF for automatically learning functional similarity estimation of gene pairs. This method calculates the functional similarity by learning the embedding vector representations of GO annotations and gene products. The results show that deepSimDEF outperforms other methods on tasks related to protein-protein interactions, gene co-expression, and sequence homology.
Article
Biochemical Research Methods
Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
Summary: This paper introduces the GrAPFI-GO method, which enhances the automatic annotation performance of protein functions by integrating semantic similarity and hierarchical relations between GO terms in a graph. Experimental results suggest that the proposed semantic hierarchical post-processing potentially improves the performance of GrAPFI-GO and other annotation tools as well.
BMC BIOINFORMATICS
(2022)
Article
Orthopedics
Daneil C. Feldmann, Masouda Rahim, Mathijs A. M. Suijkerbuijk, Mary-Jessica N. Laguette, Pawel Cieszczyk, Krzysztof Ficek, Kinga Huminska-Lisowska, Charlotte K. Hager, Evalena Stattin, Kjell G. Nilsson, Javier Alvarez-Rumero, Nir Eynon, Julian Feller, Oren Tirosh, Michael Posthumus, Emile R. Chimusa, Malcolm Collins, Alison September
Summary: Polymorphisms in VEGFA and KDR have been linked to ACL injury risk. Specific genotypes in the VEGFA gene were significantly associated with increased ACL risk, while certain haplotypes were linked to reduced risk, supporting the role of genetic factors in ACL susceptibility.
JOURNAL OF ORTHOPAEDIC RESEARCH
(2022)
Article
Biochemical Research Methods
M. Taariq Salie, Jing Yang, Carlos R. Ramirez Medina, Liesl J. Zuhlke, Chishala Chishala, Mpiko Ntsekhe, Bernard Gitura, Stephen Ogendo, Emmy Okello, Peter Lwabi, John Musuku, Agnes Mtaja, Christopher Hugo-Hamman, Ahmed El-Sayed, Albertino Damasceno, Ana Mocumbi, Fidelia Bode-Thomas, Christopher Yilgwan, Ganiyu A. Amusa, Esin Nkereuwem, Gasnat Shaboodien, Rachael Da Silva, Dave Chi Hoo Lee, Simon Frain, Nophar Geifman, Anthony D. Whetton, Bernard Keavney, Mark E. Engel
Summary: By using SWATH-MS, this study identified several biomarkers that showed significant changes in protein expression levels in patients with RHD, indicating a persistent inflammatory response. These biomarkers have the potential to be used as tools for recognizing different degrees of ongoing inflammation in RHD patients.
CLINICAL PROTEOMICS
(2022)
Correction
Microbiology
Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Michelle du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien, Adam Godzik, Jonathan M. Blackburn, David L. Tabb, Linda-Gail Bekker, Heather B. Jaspan, Jo-Ann S. Passmore, Lindi Masson
Article
Genetics & Heredity
C. Victor Jongeneel, Maritha J. Kotze, Archana Bhaw-Luximon, Faisal M. Fadlelmola, Yasmina J. Fakim, Yosr Hamdi, Samar Kamal Kassim, Judit Kumuthini, Victoria Nembaware, Fouzia Radouani, Nicki Tiffin, Nicola Mulder
Summary: This study conducted a survey among African scientists and stakeholders to evaluate their knowledge, institutional environment, and perception of genomic medicine. The findings provide guidance for African institutions to implement precision medicine approaches in their healthcare systems, including prioritization of infrastructures, translational research, information dissemination, training programs, and engagement with political stakeholders and the public.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Vincent Harrison, Saif F. Khan, Victoria Damerell, Jenna Bleloch, Kn ArulJothi, Musalula Sinkala, Katie Lennard, Nicola Mulder, Bridget Calder, Jonathan Blackburn, Sharon Prince
Summary: This study shows that tadpole tail blastema extracts (TAD) from the stream frog have anti-cancer potential against embryonal rhabdomyosarcoma (ERMS) cells. TAD inhibits cell viability, induces senescence and apoptosis, and activates DNA damage and stress signaling pathways. Furthermore, TAD inhibits tumor promoters and proteins required for cancer cell survival.
IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL
(2022)
Article
Public, Environmental & Occupational Health
Diwakar Mohan, Jean Juste Harrisson Bashingwa, Kerry Scott, Salil Arora, Sai Rahul, Nicola Mulder, Sara Chamberlain, Amnesty Elizabeth LeFevre
Summary: Kilkari is an outbound service that delivers prerecorded calls about reproductive, maternal, neonatal, and child health to families' mobile phones. Despite expanding to multiple states in India, the coverage among pregnant women remains low. While the call reach appears to be high, subscriber retention is low, highlighting broader challenges with scaling mobile health services in India.
Article
Microbiology
Nyaradzo T. L. Chigorimbo-Murefu, Matthys Potgieter, Sonwabile Dzanibe, Zikhona Gabazana, Gershom Buri, Aditya Chawla, Bokani Nleya, Abraham J. Olivier, Rushil Harryparsad, Bridget Calder, Shaun Garnett, Lungile Maziya, David A. Lewis, Heather Jaspan, Doug Wilson, Jo-Ann S. Passmore, Nicola Mulder, Jonathan Blackburn, Linda-Gail Bekker, Clive M. Gray
Summary: This pilot study shows that asymptomatic urethral sexually transmitted infections have a profound impact on the composition of male genital tract tissue, resulting in depletion of barrier integrity and immune activation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Stephanie O. M. Dyke, Kathleen Connor, Victoria Nembaware, Nchangwi S. Munung, Kathy Reinold, Giselle Kerry, Mamana Mbiyavanga, Lyndon Zass, Mauricio Moldes, Samir Das, John M. Davis, Jordi Rambla De Argila, J. Dylan Spalding, Alan C. Evans, Nicola Mulder, Jason Karamchandani
Summary: We previously proposed a structure called Consent Codes to record categories and requirements for consent-based data use. In this article, we discuss updates to the Consent Codes (v4) based on new applications, policy developments, and practical considerations, including automated consent management approaches.
Article
Cardiac & Cardiovascular Systems
Tafadzwa Machipisa, Chishala Chishala, Gasnat Shaboodien, Liesl J. Zuhlke, Babu Muhamed, Shahiemah Pandie, Jantina de Vries, Nakita Laing, Alexia Joachim, Rezeen Daniels, Mpiko Ntsekhe, Christopher T. Hugo-Hamman, Bernard Gitura, Stephen Ogendo, Peter Lwabi, Emmy Okello, Albertino Damasceno, Celia Novela, Ana O. Mocumbi, Geoffrey Madeira, John Musuku, Agnes Mtaja, Ahmed ElSayed, Huda H. M. Alhassan, Fidelia Bode-Thomas, Christopher Yilgwan, Ganiyu Amusa, Esin Nkereuwem, Nicola Mulder, Raj Ramesar, Maia Lesosky, Heather J. Cordell, Michael Chong, Bernard Keavney, Guillaume Pare, Mark E. Engel
Summary: The RHDGen Network aims to discover and validate genetic variations and biomarkers associated with the risk of rheumatic heart disease (RHD) in continental Africans. The study provides an opportunity to identify relevant genetic factors and biomarkers for RHD in Africans and further understand the causes and mechanisms of RHD susceptibility and development.
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Kevin K. Esoh, Tobias O. Apinjoh, Alfred Amambua-Ngwa, Steven G. Nyanjom, Emile R. Chimusa, Lucas Amenga-Etego, Ambroise Wonkam, Eric A. Achidi
Summary: Recent data indicate that the current genetic markers discovered can only explain a small portion of severe malaria heritability. The extensive genetic diversity among African populations suggests that significant associations may be found in Africa. In this study, a GWAS of Cameroonian participants was conducted and protective associations were identified in the CHST15 enhancer region and SOD2, highlighting the evolutionary genetics and fine-scale genetic structure within Cameroon under malaria pressure.
HUMAN MOLECULAR GENETICS
(2023)
Article
Medicine, General & Internal
Jean Juste Harrisson Bashingwa, Diwakar Mohan, Sara Chamberlain, Kerry Scott, Osama Ummer, Anna Godfrey, Nicola Mulder, Deshendran Moodley, Amnesty Elizabeth LeFevre
Summary: A proof of concept approach using machine learning was used to segment populations of pregnant women and their husbands into distinct clusters for differential digital health program design and delivery. The findings suggest that segmenting populations into clusters can improve the reach and impact of health programs.
Article
Biochemical Research Methods
Matthys J. Potgieter, Andrew J. M. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome Wendoh, David Tabb, Nicola Mulder, Jonathan Blackburn
Summary: MetaNovo is an open-source software pipeline that integrates existing tools with a custom algorithm to produce targeted protein sequence databases for mass spectrometry metaproteomic analysis as an intermediate filtering step prior to standard sequence database search approaches. The software uses open-source tools to match peptide mass spectrometry spectra to sequence database entries and can be installed in a cluster or run standalone on a Linux machine. It is relevant for analyzing protein data from multiple organisms, where the exact species composition is unknown, and provides an avenue for analysis when accurate taxonomic characterization is not available.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Editorial Material
Biotechnology & Applied Microbiology
Esra Busra Isik, Michelle D. Brazas, Russell Schwartz, Bruno Gaeta, Patricia M. Palagi, Celia W. G. van Gelder, Prashanth Suravajhala, Harpreet Singh, Sarah L. Morgan, Hilyatuz Zahroh, Maurice Ling, Venkata P. Satagopam, Annette McGrath, Kenta Nakai, Tin Wee Tan, Ge Gao, Nicola Mulder, Christian Schonbach, Yun Zheng, Javier De Las Rivas, Asif M. Khan
Summary: Given the growing demand for bioinformatics expertise in the life sciences, a collective effort is required to proactively evaluate and address the challenges of educating and training life scientists with the requisite skills and competencies.
NATURE BIOTECHNOLOGY
(2023)
Article
Mathematical & Computational Biology
Gaston K. Mazandu, Jade Hotchkiss, Victoria Nembaware, Ambroise Wonkam, Nicola Mulder
Summary: The Sickle Cell Disease Ontology (SCDO) is a knowledge base that provides information on terminology and concepts related to sickle cell disease. It aims to support researchers, patients, and clinicians by continuously updating and improving its resources.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Biotechnology & Applied Microbiology
Sarudzai Muyambo, Arinao Ndadza, Nyarai D. Soko, Bianca Kruger, Gerard Kadzirange, Emile Chimusa, Collen M. Masimirembwa, Mpiko Ntsekhe, Charles F. B. Nhachi, Collet Dandara
Summary: Pharmacogenomics is important for modern therapeutics worldwide, but its application in African clinical practice is limited. African patients often have multiple comorbidities, yet current research primarily focuses on controlled medical settings.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
