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PubMed2004

Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics.

In 2002-2003, the American College of Medical Informatics (ACMI) undertook a study of the future of informatics training. This project capitalized on the rapidly expanding interest in the role of computation in basic biological research, well characterized in the National Institutes of Health (NIH) Biomedical Information Science and Technology Initiative (BISTI) report. The defining activity of the project was the three-day 2002 Annual Symposium of the College. A committee, comprised of the authors of this report, subsequently carried out activities, including interviews with a broader informatics and biological sciences constituency, collation and categorization of observations, and generation of recommendations. The committee viewed biomedical informatics as an interdisciplinary field, combining basic informational and computational sciences with application domains, including health care, biological research, and education. Consequently, effective training in informatics, viewed from a national perspective, should encompass four key elements: (1). curricula that integrate experiences in the computational sciences and application domains rather than just concatenating them; (2). diversity among trainees, with individualized, interdisciplinary cross-training allowing each trainee to develop key competencies that he or she does not initially possess; (3). direct immersion in research and development activities; and (4). exposure across the wide range of basic informational and computational sciences. Informatics training programs that implement these features, irrespective of their funding sources, will meet and exceed the challenges raised by the BISTI report, and optimally prepare their trainees for careers in a field that continues to evolve.

Computational Biology↗
PubMed2000

Human genetics in health care.

UNLABELLED: The Human Genome Project, the mapping of our 100,000 genes and the sequencing of all of our DNA, will have major impact on biomedical research and the whole of therapeutic and preventive health care. The tracing of genetic diseases to their molecular causes is rapidly expanding diagnostic and preventive options, while the increased insights into molecular pathways open tremendous perspectives for pharmacological and genetic therapies. The design of animal model systems for the functional study of disease and development and the use of bioinformatics and biostatistics to improve our pattern recognition abilities are greatly accelerating progress. However, the optimal value from the current explosion of 'data mining' possibilities will only be gained when the basic data are made and kept publicly accessible, while at the same time safeguarding the protection of intellectual property arising from downstream inventions. This is one of the goals of the international Human Genome Organisation, established 10 years ago to assist coordinating data acquisition and exchange and societal implementation of the genome project. Additional points of major attention in this historic endeavour are the safeguarding of a worldwide balance in the contribution and benefits to countries and populations, the prevention of stigmatisation and discrimination of individuals and groups and the maintenance of respect for the diversity of our world's cultures and traditions. CONCLUSION: The acquisition and use of genomic information for health care benefit should be seen in the light of a worldwide improvement without prejudice.

Ethics, Medical↗
PubMed2004

Structural bioinformatics study of PNP from Schistosoma mansoni.

The parasite Schistosoma mansoni lacks the de novo pathway for purine biosynthesis and depends on salvage pathways for its purine requirements. Schistosomiasis is endemic in 76 countries and territories and amongst the parasitic diseases ranks second after malaria in terms of social and economic impact and public health importance. The PNP is an attractive target for drug design and it has been submitted to extensive structure-based design. The atomic coordinates of the complex of human PNP with inosine were used as template for starting the modeling of PNP from S. mansoni complexed with inosine. Here we describe the model for the complex SmPNP-inosine and correlate the structure with differences in the affinity for inosine presented by human and S. mansoni PNPs.

Amino Acid Sequence↗
PubMed2005

[Identification and analysis of a mouse gene homologous to human hepatitis B virus pre-S1 protein-binding protein using the bioinformatics method].

OBJECTIVE: To clone and identify the mouse gene homologous to human hepatitis B virus (HBV) pre-S1 protein-binding protein (PS1BP). METHODS: The human PS1BP cDNA sequence was used as the reference sequence to search homologous mouse cDNA sequence from GenBank established by National Center for Biotechnology (NCBI), National Institute of Health (NIH), for its homologous cDNA sequences of mouse by BLASTn tool. The characteristics of mouse PS1BP protein primary structure were predicted by online software. Finally the genomic DNA structure of mouse PS1BP was deduced and compared. RESULTS: The mouse PS1BP was identified and consisted of 1455 nt, coding a protein of 484 aa. The identity of human and mouse PS1BP protein is 84.92% (411/484). The genomic DNA of mouse PS1BP consisted of 3 exons and 2 introns. CONCLUSION: The identification and characterization of mouse PS1BP cDNA and genomic DNA pave a way for further study of their structures and functions.

Amino Acid Sequence↗
PubMed2025

A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.

PURPOSE: The Undiagnosed Diseases Network is a National Institutes of Health funded research study that aims to solve a broad clinical spectrum of challenging rare disease cases. Participants receive care from multiple clinical specialists, who collaborate to perform deep phenotyping and state-of-the-art multiomics analyses. As bioinformatics of short-read sequencing has matured, the discovery of repeat expansion disorders (REDs) is accelerating. REDs comprise approximately 60 characterized disorders, which exhibit a broad spectrum of phenotypes. Thus, a largely unbiased genome-wide approach in a phenotypically diverse sample will add to the diagnostic depth, explore the limits of short-read genome analysis, and establish novel candidate RED loci. METHODS: Here, we present a genome-wide analysis of repeat expansions conducted on 1018 genomes from the Undiagnosed Diseases Network. By leveraging 2 distinct bioinformatics tools, ExpansionHunter Denovo and STRling, we showed that repeat expansions can be accurately detected in short-read genomes. RESULTS: We demonstrated that a genotype-first approach can diagnose atypical cases of known REDs and provide valuable clinical insights. We present clinical details on participants with expansions in ATXN7, DMPK, FMR1, GLS, HTT, RFC1, AFF3, and MARCH6. Importantly, we highlight 2 cases of juvenile Huntington disease that were discovered through our analysis. Finally, we present a list of novel candidate short tandem repeats (TR) that could potentially be pathogenic if expanded. CONCLUSION: Importantly, our approach showcases the bioinformatic advancements in genome analysis for RED detection and highlights its practical applications.

Humans↗
PubMed2025

Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective.

INTRODUCTION: Antibiotic resistance, particularly carbapenem-resistant Klebsiella pneumoniae (CRKP), poses significant clinical and environmental threats, especially in urban aquatic ecosystems and hospital wastewaters. OBJECTIVES: This study aims to analyze the epidemiological and genomic features of CRKP isolates in urban aquatic environments and evaluate their public health and environmental impacts. METHODS AND RESULTS: Water samples were collected from 113 rivers and 3 hospitals in China, Sri Lanka, and Nepal to isolate carbapenem-resistant Klebsiella spp. isolates. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics analyses were performed to characterize resistance phenotypes, antibiotic resistance genes (ARGs), and evolutionary trends. Big data analysis further elucidated the genomic characteristics of CRKP in global water sources, and Galleria mellonella larvae were used to assess virulence. Statistical analysis validated the findings. A total of 192 carbapenem-resistant Klebsiella spp. isolates were identified from urban aquatic ecosystems in China (n = 60) and Nepal (n = 132), with CRKP (n = 161) being the predominant species. All CRKP isolates exhibited a multidrug-resistant phenotype, yet significant differences in resistance profiles and associated ARGs were observed between isolates from the two countries. Nine carbapenem resistance genes (CRGs) were detected, with blaNDM-1 being the most prevalent (57.8 %). Correlation analysis revealed a strong association between these CRGs and multiple Inc-type plasmids. Global genomic analysis of CRKP from water sources across eight countries identified ten distinct CRGs across 45 serotypes, with KL64 being the most predominant. Notably, carbapenem-resistant hypervirulent Klebsiella pneumoniae was detected in water samples from Nepal. CONCLUSION: Our findings highlight significant regional disparities in CRKP prevalence and ARG dissemination across urban aquatic environments, with Nepal showing the highest prevalence, particularly in untreated rivers. China exhibited lower prevalence but distinct resistance gene profiles, while no CRKP was detected in Sri Lanka, underscoring the impact of environmental management and healthcare infrastructure on ARG spread.

Humans↗
PubMed1998

The Human Genome Project and the role of genetics in health care.

The Human Genome Project, the mapping of our 100,000 genes and the sequencing of all of our DNA, will have major impact on biomedical research and the therapeutic and preventive health care. The tracing of genetic diseases to their molecular causes is rapidly expanding diagnostic and preventive options, while the increased insights into molecular pathways open tremendous perspectives for pharmacological and genetic therapies. The design of animal model systems for the functional study of disease and development of bioinformatics and biostatistics to improve our pattern recognition abilities are greatly accelerating progress. However, the optimal value from the current explosion of 'data mining' possibilities will only be gained when the basic data are made and kept publicly accessible, at the same time preventing the jeopardisation of the protection of intellectual property, arising from downstream inventions. This is one of the goals of HUGO, the international Human Genome Organisation, established 9 years ago to assist coordinating data acquisition and exchange and societal implementation of the genome project. Additional points of major importance in this historic endeavour are the safeguarding of a worldwide balance in the contribution and benefits to countries and population, the prevention of stigmatisation and discrimination of individuals and groups and the maintenance of respect for the priceless diversity of our world's cultures and traditions.

Delivery of Health Care↗
PubMed2025

Unveiling the Genomic Landscape of Escherichia coli O1:K1:H7 ST59 in Non-complicated Urinary Infections from Colombia Through Whole-Genome Sequencing.

Escherichia coli (E. coli) is a Gram-negative bacterium known for causing both intestinal and extraintestinal infections in humans. Among extraintestinal infections, urinary tract infections (UTIs) are particularly prevalent and impactful. In Colombia, limited information is available regarding the molecular epidemiology of E. coli. This lack of data hinders the understanding of the local epidemiological landscape and the identification of pathogenic lineages that may contribute to public health concerns. This study aimed to characterize an E. coli strain isolated from a 24-year-old female patient with a community-acquired lower UTI, focusing on genotypic analysis through whole-genome shotgun sequencing (WGSS) and subsequent bioinformatics investigations. The identified strain belongs to phylogroup F, with serotype O1:H7 and sequence type (ST) 59. Several virulence factors, including traT and afimbrial adhesins (afaC), were identified, with afaC being notably uncommon in ST59 phylogroup F. In addition, an antibiotic susceptibility test was performed, and the isolate was found to be sensitive to all the antibiotics tested. This work contributes to the understanding of E. coli phylogroup F in Colombia and provides valuable genomic data, shedding light on the virulence profile of this strain in lower urinary tract infections.

Female↗
PubMed2002

The era of genomics: impact on sepsis clinical trial design.

OBJECTIVE: This article aims to address the predictable impact of genetics on the design of clinical trials in the field of critical care medicine, with emphasis on the pathophysiology of sepsis and its treatment. DATA SOURCES: Published articles reporting studies on sepsis and septic shock or assessing the influence of genetics and pharmacogenomics in the treatment of critical illnesses. DATA ANALYSIS: Because most common diseases including sepsis have been shown to be influenced by inherited differences in our genes, completion of the Human Genome Project and the concomitant publication of the human single nucleotide polymorphism map both contribute to change our approach to medicine. Advances in genotyping techniques and bioinformatics enabling detection of single nucleotide polymorphisms have caused an explosion in pharmacogenomics-the research dealing with the interactions of an individual's genotype and the outcome of a drug therapy. Pharmacogenomics will undoubtedly be used to improve future health care and clinical research in different ways. Whereas treatment allocation has been based mainly on phenotype, genetic characterization will help researchers to identify suitable subjects for clinical trials, to facilitate interpretation of the results of clinical trials, and to identify novel targets for future drugs or new markets for current products. As interindividual variability in drug response is a substantial clinical problem, the second major objective of pharmacogenomic research is to decrease adverse responses to therapy through determination of adequate therapeutic targets and genetic polymorphisms that alter drug specificity and toxicity. Ultimately, genetic information will be used to select the most effective therapeutic agent and the optimal dosage to elicit the expected drug response for a given individual. Implementation of genetic criteria for stratification of patient populations and individual assessment of treatment risks and benefits emerges as a major challenge to the pharmaceutical industry. CONCLUSIONS: In the future, technologies such as gene chip array will enhance genetic medicine and provide novel insights into a patient's susceptibility to disease, enabling a better assessment of prognostic risk factors, quicker diagnosis, and accurate prediction of individual responsiveness to drugs. The predictable consequences of such an approach on the prevention and treatment of diseases could revolutionize medicine.

Animals↗
PubMed2005

Bioinformatics meets clinical informatics.

The field of bioinformatics has exploded over the past decade. Hopes have run high for the impact on preventive, diagnostic, and therapeutic capabilities of genomics and proteomics. As time has progressed, so has our understanding of this field. Although the mapping of the human genome will certainly have an impact on health care, it is a complex web to unweave. Addressing simpler "Single Nucleotide Polymorphisms" (SNPs) is not new, however, the complexity and importance of polygenic disorders and the greater role of the far more complex field of proteomics has become more clear. Proteomics operates much closer to the actual cellular level of human structure and proteins are very sensitive markers of health. Because the proteome, however, is so much more complex than the genome, and changes with time and environmental factors, mapping it and using the data in direct care delivery is even harder than for the genome. For these reasons of complexity, the expected utopia of a single gene chip or protein chip capable of analyzing an individual's genetic make-up and producing a cornucopia of useful diagnostic information appears still a distant hope. When, and if, this happens, perhaps a genetic profile of each individual will be stored with their medical record; however, in the mean time, this type of information is unlikely to prove highly useful on a broad scale. To address the more complex "polygenic" diseases and those related to protein variations, other tools will be developed in the shorter term. "Top-down" analysis of populations and diseases is likely to produce earlier wins in this area. Detailed computer-generated models will map a wide array of human and environmental factors that indicate the presence of a disease or the relative impact of a particular treatment. These models may point to an underlying genomic or proteomic cause, for which genomic or proteomic testing or therapies could then be applied for confirmation and/or treatment. These types of diagnostic and therapeutic requirements are most likely to be introduced into clinical practice through traditional forms of clinical practice guidelines and clinical decision support tools. The opportunities created by bioinformatics are enormous, however, many challenges and a great deal of additional research lay ahead before this research bears fruit widely at the care delivery level.

Computational Biology↗
PubMed2005

Detection of one VH antibody sequence in both healthy donors and urticaria patients.

We have previously isolated anti-FcepsilonRIalpha autoantibodies from phage libraries of healthy donors and urticaria patients. Strikingly, the same antibody, LTMalpha15, was isolated from both libraries. Sequence analysis revealed a germline configuration of the LTMalpha15 variable heavy (V(H)) chain with a slightly mutated variable light (V(L)) chain supporting its classification as a natural autoantibody. Distribution analysis of anti-FcepsilonRIalpha autoantibodies by functional or serological tests delivered conflicting data. For this reason we have developed a new real-time PCR to analyse the distribution of LTMalpha15V(H) in healthy donors and urticaria patients. Our new bioinformatic program permitted the design of a minor groove binder (MGB) TaqMan probe that specifically detected the LTMalpha15V(H). We were able to demonstrate a broad range of rearranged V(H) gene copy number without any correlation to the state of health. Monitoring LTMalpha15V(H) gene copy number in a single donor over a period of 70 days revealed a time-related fluctuation of circulating B cells carrying LTMalpha15V(H). We propose that our real-time PCR may serve as a model for the quantification of natural antibody sequences at a monoclonal level.

Autoantibodies↗
PubMed2000

Future opportunities for life science programs in space.

Most space-related life science programs are expensive and time-consuming, requiring international cooperation and resources with trans-disciplinary expertise. A comprehensive future program in "life sciences in space" needs, therefore, well-defined research goals and strategies as well as a sound ground-based program. The first half of this review will describe four key aspects such as the environment in space, previous accomplishments in space (primarily focusing on amphibian embryogenesis), available resources, and recent advances in bioinformatics and biotechnology, whose clear understanding is imperative for defining future directions. The second half of this review will focus on a broad range of interdisciplinary research opportunities currently supported by the National Aeronautics and Space Administration (NASA), National Institute of Health (NIH), and National Science Foundation (NSF). By listing numerous research topics such as alterations in a diffusion-limited metabolic process, bone loss and skeletal muscle weakness of astronauts, behavioral and cognitive ability in space, life in extreme environment, etc., we will attempt to suggest future opportunities.

Animals↗
PubMed2007

[Burkitt's and Burkitt-like lymphoma. Molecular definition and value of the World Health Organisation's diagnostic criteria].

Among aggressive mature B-cell lymphomas, a reproducible morphological and immunohistological distinction between Burkitt's lymphoma and diffuse large B-cell lymphoma (centroblastic variant) is impossible in a substantial number of cases. The German reference centres for hematopathology collected 220 retrospective cases of aggressive mature B-cell lymphoma whose classification according to the current World Health Organisation criteria was reviewed. Gene expression analysis (Affymetrix) was performed in all cases and chromosomal translocations were determined using fluorescence in situ hybridization. Chromosomal losses and gains were analysed by matrix comparative genomic hybridisation and clinical data were successfully collected for most patients. The application of a novel bioinformatics method led to the identification of a stable and reproducible gene expression signature specific for Burkitt's lymphoma. A total of 44 cases were identified by this molecular signature [designated molecular Burkitt's lymphoma (mBL)]. These molecular Burkitt's lymphomas showed the morphology and immunohistology of classical or atypical Burkitt's lymphoma cases in 29 instances. However, 15 of the molecular Burkitt's lymphoma cases had the morphology of diffuse large B-cell lymphoma or could not be further specified. All molecular Burkitt's lymphomas showed an expression of BCL-6 and CD10, but a MYC translocation was not demonstrable in more than 10% of cases. Of significance is that more than 20% of the molecular Burkitt's lymphomas expressed BCL-2, although weakly in most instances. Our data demonstrate that: (1) the morphological, immunophenotypical and genetic spectrum of Burkitt's lymphoma is broader than previously expected, and (2) our molecular Burkitt's lymphoma signature enables a more precise and extended definition this lymphoma.

Burkitt Lymphoma↗
PubMed2004

Morbidity in schistosomiasis: an update.

PURPOSE OF REVIEW: Schistosomiasis is an important poverty-related health problem and more than 200 million people are infected. This review summarizes papers from April 2003 to June 2004 with a focus on schistosomiasis morbidity and the various factors that affect the level of morbidity in endemic populations. The aim is to provide an update on the current state of knowledge and, hopefully, thereby stimulate continued research interest in this important area. RECENT FINDINGS: Research into the immune responses associated with severe morbidity has provided new insights into the mechanisms of immune regulation as well as the role of genetic predisposition to periportal fibrosis. Malaria and schistosomiasis are co-endemic and co-infection with malaria may increase the level of morbidity in hepatosplenic schistosomiasis, and alter the host immune response towards schistosome antigens. Schistosome infections may render the host more susceptible to human immunodeficiency virus infection by either interfering with immune responses or increasing the risk of transmission due to genital lesions. An important advance in schistosomiasis research, and parasite genomics, is the recent availability of two major Schistosoma mansoni and Schistosoma japonicum DNA bioinformatic resources. SUMMARY: Significant advances have been achieved in our understanding of the epidemiology, immunology and genetics of schistosomiasis, and the various factors that may influence morbidity. However, good research is vital for sustainable disease control, and continued progress requires a critical mass of researchers with a range of expertise from basic parasite biology to public-health interventions. It is therefore important to strengthen research capacity in endemic countries.

Animals↗
PubMed2026

Identification of circulating parasite and host biomarkers in the serum proteome of Trypanosoma vivax-infected sheep under immunosuppression.

Bovine trypanosomiasis, caused by Trypanosoma vivax, presents a major threat to livestock health, primarily due to the lack of efficient field diagnostic tools. This study aimed to identify potential parasite and host-derived biomarkers through a longitudinal proteomic analysis of serum from sheep experimentally infected with a T. vivax isolate. Utilizing LC-MS/MS and bioinformatics, 154 proteins were identified, comprising 150 host (Ovis aries) and four pathogen proteins. Principal Component Analysis (PCA) demonstrated a clear separation of samples according to infection stages: Control, Infection (15 parasites/field), and Peak Infection (30-60 parasites/field) Among the parasite proteins, TvY486_0014340, TvY486_0040500, and TvY486_0042480 were identified as candidate antigens for future evaluation. In silico analysis revealed these proteins contain multiple B-cell epitopes with no cross-reactivity to related Trypanosoma species, supporting their potential for immunodiagnostic development. Additionally, three host proteins-folate receptor 3 (FOLR3) and complement components C1QA and C1QC-were significantly modulated across all infection phases. The upregulation of FOLR3 likely reflects a compensatory response to parasite-induced anemia, while the downregulation of C1Q components suggests immune evasion strategies. These findings highlight specific parasite antigens and host regulatory patterns that may serve as candidate biomarkers for the diagnosis and monitoring of T. vivax infection, facilitating the development of improved point-of-care assays.

Animals↗
PubMed2026

Glycoinformatic Profiling of Label-Free Intact Heparan Sulfate Oligosaccharides.

Heparan sulfates (HSs) are a group of heterogenous linear, sulfated polysaccharides that play a role in health and many diseases, including cancer, cardiovascular, and kidney diseases. The structural variety of HS has greatly challenged the development and utility of HS analytics, particularly for native (nondepolymerized) structures, leaving a significant gap in HS technologies for clinical application. Mass spectrometry-based profiling with bioinformatics offers an approach that can retain variety in large datasets. Using healthy human plasmas, we developed a mass spectrometry glycoprofiling approach for native HS oligosaccharides, which retains the structural complexity of each individual HS chain and generates an HS "index" (or Heparan-ome) for each patient. As a proof of concept, analysis of 53 plasma samples ranging from four groups of kidney disease patients revealed a new subset cluster (21%, 4/19) of membranous glomerulopathy patients with distinct HS profiles, highlighting the potential of HS glycoprofiling as a powerful new approach to clinical practice, which warrants future development into quantitative oligosaccharide glycosaminoglycanomics and clinical diagnostics of kidney and other diseases.

Humans↗
PubMed2026

Regulators of interferon-responsive microglia uncovered by Genome-wide CRISPRi screening.

Microglia dynamically support brain health through the induction of specialized activation states in response to injury or disease. Activation of the interferon-responsive microglia (IRM) state has been identified across neurodevelopmental windows, age-related cognitive decline, and neurodegenerative diseases. Functionally, IRM have been linked to synaptic pruning, dead cell removal, and neuroinflammation, making this state critical to brain homeostasis. While the functional importance of this state is becoming increasingly clear, our understanding of the regulatory networks that govern IRM induction remain incomplete. To systematically identify genetic regulators of the IRM state, we conducted a genome-wide CRISPR interference screen in human iPSC-derived microglia using IFIT1 as a representative IRM marker. We identified 772 genes that modulate IRM, including canonical type I interferon signaling genes (IFNAR2, TYK2, STAT1/2, USP18) and newly described regulators. We uncovered a non-canonical role for the CCR4-NOT transcription complex subunit 10, CNOT10, in IRM activation. This work provides a comprehensive resource that can be applied to dissect the functions of interferon-responsive microglia and highlights both established and novel targets for modulating microglial interferon signaling in health and disease.

Computational biology and bioinformatics↗