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Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data ... the implementation of a state-of-the-art Natural Language Processing system tha...
Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this...
Natural Language Processing (NLP) has been shown effective to...
The Enteropathogen Resource Integration Center (ERIC; http://www.ericbrc.org) has a goal of providing bioinformatics support for the scientific communi...
The abundance of biomedical text data coupled with advances in natural language processing (NLP) is resulting in novel biomedical ... are reliant on the availability of domain-specific language models (LMs) that ...
Many biomedical natural language processing systems demonstrated large differences between their previously...
We present an extension of the TM tool, which utilizes natural language processing (NLP) for analyzing the context of ... the global low-resolution docking scan was post-processed, separately, by constraints from...
Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local r...
We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification....
Natural language processing (NLP) applications are increasingly important in...
Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance...
Applications of Natural Language Processing (NLP) technology to biomedical texts have...subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are chara...
Pre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to ... , few studies focused on enriching such protein language models by jointly learnin...
The growing recognition of the microbiome’s impact on human health and well-being has prompted extensive research into discovering the links between microbiome dysbiosis and disease (healthy) states. However, thi...
Longitudinal data on key cancer outcomes for clinical research, such as response to treatment and disease progression, are not captured in standard cancer registry reporting. Manual extraction of such outcomes fr...
Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...
Protein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signa...
It has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word ... , and that the algorithms originally developed for natural
Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information ...
Monoclonal antibodies (mAbs) have been used as therapeutic agents, which must overcome many developability issues after the discovery from in vitro display libraries. Especially, polyreactive mAbs can strongly...
Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data ti...
Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis...
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. Although...
We introduced a novel way to represent protein sequences as continuous vectors (embeddings) by using the language model ELMo taken from natural language processing. By modeling protein sequences, ELMo effectively...
Decisions in healthcare usually rely on the goodness and completeness of data that could be coupled with heuristics to improve the decision process itself. However, this is often an incomplete process. Structured...
Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i...
Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...
Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to ... the neural network and large scale pre-trained language model have largely improved its perf...
Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...
This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for bi...
CoQUAD is a question-answering system that mines COVID-19 literature using natural language processing techniques to help the research community find...
Glaucoma can cause irreversible blindness to people’s eyesight. Since there are no symptoms in its early stage, it is particularly important to accurately segment the optic disc (OD) and optic cup (OC) from fu...
Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that pr...
We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein...bibliosphere. We illustrate the extent of the desc...
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...
Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...
We verified that typographical errors in unstructured text negatively affect the performance of natural language processing tasks. The proposed method of a typo...
During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they c...
Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...
Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4–5 times underrepresented compared to non-TMPs. Today’s top ...
One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...
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 ... the art involves the use of neural netw...
The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in th...
The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors in...
Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Que...
SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization co...
Genomic functional information is valuable for biomedical research. However, such information frequently needs to be extracted from the scientific literature and structured in order to be exploited by automatic s...
In the era of information overload, natural language processing (NLP) techniques are increasingly needed to...
The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been gen...
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2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)
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12 days submission to first editorial decision for all manuscripts (Median)
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