A5081185204- Malaria Research and Control
- Invertebrate Immune Response Mechanisms
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Insect Resistance and Genetics
- Viral Infectious Diseases and Gene Expression in Insects
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- vaccines and immunoinformatics approaches
- SARS-CoV-2 and COVID-19 Research
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
- Viral Infections and Immunology Research
- Gene expression and cancer classification
- Biomedical and Engineering Education
- interferon and immune responses
- COVID-19 epidemiological studies
- Biotechnology and Related Fields
- Vaccine Coverage and Hesitancy
- Species Distribution and Climate Change
- AI in cancer detection
- Radiomics and Machine Learning in Medical Imaging
- Machine Learning in Bioinformatics
- Cancer, Lipids, and Metabolism
University of Michigan–Ann Arbor
2022-2024
Center for Global Health
2022-2024
Michigan Medicine
2023-2024
St. Paul's Hospital Millennium Medical College
2024
University of Notre Dame
2013-2022
Institut Curie
2020
IBM Research - Africa
2016-2018
IBM (United States)
2015-2016
University of Pennsylvania
2015
California University of Pennsylvania
2015
The Metagenomics and Metadesign of the Subways Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised experts across many fields, including genomics, data analysis, engineering, public health, architecture. ultimate goal MetaSUB to improve city utilization planning through detection, measurement, design metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, human activity, longitudinal,...
Scientific research plays a key role in the advancement of human knowledge and pursuit solutions to important societal challenges. Typically, occurs within specific institutions where data are generated subsequently analyzed. Although collaborative science bringing together multiple is now common, such collaborations analytical processing often performed by individual researchers team, with only limited internal oversight critical analysis workflow prior publication. Here, we show how...
Abstract The spread of Plasmodium falciparum multidrug resistance highlights the urgency to discover new targets and chemical scaffolds. Unfortunately, lack experimentally validated functional information about most P. genes remains a strategic hurdle. Chemogenomic profiling is an established tool for classification drugs with similar mechanisms action by comparing drug fitness profiles in collection mutants. Inferences can be obtained associations between shifts specific genetic changes In...
Abstract Background Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 Dd2 diverge their proliferation rates, here use quantitative trait loci mapping 34 progeny from a cross between these parent clones along with integrative bioinformatics identify genetic candidate control...
Although maps of intracellular interactions are increasingly well characterized, little is known about large-scale host-pathogen protein interactions. The investigation can reveal features pathogenesis and provide a foundation for the development drugs disease prevention strategies. A compilation experimentally verified between HIV-1 human proteins set HIV-dependency factors (HDF) allowed insights into topology intricate interplay viral host on large scale. We found that targeted HDF appear...
Transcriptional responses to small molecules can provide insights into drug mode of action (MOA). The capacity the human malaria parasite, Plasmodium falciparum, respond specifically transcriptional perturbations has been unclear based on past approaches. Here, we present most extensive profiling date parasite's responsiveness thirty-one chemically and functionally diverse molecules. We exposed two laboratory strains parasite P. falciparum brief treatments associated with biological effects...
The paradigm of resistance evolution to chemotherapeutic agents is that a key coding mutation in specific gene drives particular drug. In the case anti-malarial drug chloroquine (CQ), transporter pfcrt associated with resistance. Here, we apply series analytical steps expression data from our lab and leverage 3 independent datasets identify pfcrt-interacting genes. Resulting networks provide insights into pfcrt's biological functions regulation, as well divergent phenotypic effects its...
Cancer and malaria exemplify two maladies historically assigned to separated research spaces. Cancer, on the one hand, ranks among top priorities in agenda of developed countries. Its rise is mostly explained by ageing these populations linked environment lifestyle. Malaria, other represents a major health burden for developing countries Southern Hemisphere. These diseases also belong separate fields medicine: non-communicable cancer communicable malaria.
Abstract Background Serum aspartate transaminase (sAST) level is used routinely in conjunction with other clinical assays to assess liver health and disease. Increasing evidence suggests that sAST associated all-cause mortality has prognostic value several cancers, including gastrointestinal urothelial cancers. Here, we undertake a systems approach unravel molecular connections between AST cancer prognosis, metabolism, immune signatures at the transcriptomic proteomic levels. Methods We...
The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. was presented to the community framework sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), effort evaluate status systems biology modeling methodologies. Nucleotide-specific activity obtained by measuring fluorescence fused upstream yellow protein inserted same genomic site yeast Saccharomyces...
Gene expression DNA microarrays have been vital for characterizing whole-genome transcriptional profiles. Nevertheless, their effectiveness relies heavily on the accuracy of genome sequences, annotation gene structures, and sequence-dependent performance individual probes. Currently available arrays malaria parasite Plasmodium falciparum rely an average 2 probes per gene, usually positioned near 3' end genes; consequently, existing designs are prone to measurement bias cannot capture...
High-throughput techniques have become a primary approach to gathering biological data. These data can be used explore relationships between genes and guide development of drugs other research. However, the deluge contains an overwhelming amount unknown information about organism under study. Therefore, clustering is common first step in exploratory analysis high-throughput We present supervised learning that utilises known gene-gene interaction improve results for already commonly...
A fundamental goal of systems biology is to create models that describe relationships between biological components. Networks are an increasingly popular approach this problem. However, a scientist interested in modeling (e.g., gene expression) data as network quickly confounded by the problem: how construct network? It fairly easy network, but it for problem being considered? This important with three issues: How weight edges order capture actual interactions? What effect type experiment...
We augmented existing computationally predicted and experimentally determined interactions with evolutionarily conserved between proteins of the malaria parasite, P. falciparum, human host. In a validation step, we found that interacting host-parasite protein pairs were specifically expressed in host tissues where both parasite are known to be active. compared verified very different pathogen, HIV-1. Both pathogens use their repertoire combinatorial manner, providing broad connection...
<ns4:p>The quantitative prediction of transcriptional activity genes using promoter sequence is fundamental to the engineering biological systems for industrial purposes and understanding natural variation in gene expression. To catalyze development new algorithms this purpose, Dialogue on Reverse Engineering Assessment Methods (DREAM) organized a community challenge seeking predictive models given normalized data 90 ribosomal protein promoters driving expression fluorescent reporter gene....
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While large language models (LLMs) have shown promise for medical question answering, there is limited work focused on tropical and infectious disease-specific exploration. We build an opensource diseases (TRINDs) dataset, expanding it to include demographic semantic clinical consumer augmentations yielding 11000+ prompts. evaluate LLM performance these, comparing generalist LLMs, as well outcomes human experts. demonstrate through systematic experimentation, the benefit of contextual...
Background: Little is known about the determinants of disease progression among African patients with chronic HBV infection. Methods: We used machine-learning models longitudinal data to establish predictive algorithms in a well-characterized cohort Ethiopian HBV-infected without baseline liver fibrosis. Disease was defined as an increase stiffness >7.9 kPa or initiation treatment based on meeting eligibility criteria. Results: Twenty-four 551 (4.4%) experienced after median follow-up...
Nucleosides are fundamental building blocks of DNA and RNA in all life forms viruses. In addition, natural nucleosides their analogs critical prebiotic chemistry, innate immunity, signaling, antiviral drug discovery artificial synthesis / sequences. Combined with the fact that quantitative structure activity relationships (QSAR) have been widely performed to understand activity, nucleoside could be used benchmark generative molecular design. Here, we undertake first design using an approach...
Clustering is a common step in the analysis of microarray data. Microarrays enable simultaneous high-throughput measurement expression level genes. These data can be used to explore relationships between genes and guide development drugs further research. A typical first these use an agglomerative hierarchical clustering algorithm on correlation all gene pairs. While this simple approach has been successful it fails identify many genetic interactions that may important for drug design other...