A5036736055- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Machine Learning in Bioinformatics
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Pharmacogenetics and Drug Metabolism
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- Advanced Proteomics Techniques and Applications
- Machine Learning in Materials Science
- Endoplasmic Reticulum Stress and Disease
- Pancreatic function and diabetes
- Advanced Graph Neural Networks
- Chromosomal and Genetic Variations
- Coastal wetland ecosystem dynamics
- Click Chemistry and Applications
- Aquaculture disease management and microbiota
- Chemical Synthesis and Analysis
Johnson & Johnson (United States)
2023
Janssen (United States)
2023
King Abdullah University of Science and Technology
2011-2022
Jackson Laboratory
2017-2021
Bioscience Research
2012-2015
Biologie cellulaire et Cancer
2013
Inserm
2013
École Nationale Supérieure des Mines de Paris
2013
Centre National de la Recherche Scientifique
2013
Marshfield Clinic
2012
Abstract Despite half a century of research, the biology dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches study are often stymied due their large, multi-gigabase genomes. Members genus Symbiodinium photosynthetic endosymbionts stony corals that provide foundation coral reef ecosystems. Their smaller genome sizes an opportunity interrogate evolution functionality dinoflagellate genomes endosymbiosis. We...
Models of transcription factor (TF) binding sites provide a basis for wide spectrum studies in regulatory genomics, from reconstruction networks to functional annotation transcripts and sequence variants. While TFs may recognize different patterns conditions, it is pragmatic have single generic model each particular TF as baseline practical applications. Here we present the expanded enhanced version HOCOMOCO (http://hocomoco.autosome.ru http://www.cbrc.kaust.edu.sa/hocomoco10), collection...
Abstract Motivation Finding computationally drug–target interactions (DTIs) is a convenient strategy to identify new DTIs at low cost with reasonable accuracy. However, the current DTI prediction methods suffer high false positive rate. Results We developed DDR, novel method that improves DDR based on use of heterogeneous graph contains known multiple similarities between drugs and target proteins. applies non-linear similarity fusion combine different similarities. Before fusion, performs...
Individual plasma proteins have been identified as minimally invasive biomarkers for lung cancer diagnosis with potential utility in early detection. Plasma proteomes provide insight into contributing biological factors; we investigated their future prediction.The Olink® Explore-3072 platform quantitated 2941 496 Liverpool Lung Project samples, including 131 cases taken 1-10 years prior to diagnosis, 237 controls, and 90 subjects at multiple times. 1112 significantly associated haemolysis...
Abstract In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when research focus to capitalize on repositioning existing drugs. However, developing such computational methods not an easy task, but much needed, as current that predict potential suffer from high false-positive rates. Here we introduce DTiGEMS+, method predicts D rug– T arget i nteractions using G raph E mbedding, graph M ining, and S imilarity-based...
Abstract Chromatin interaction studies can reveal how the genome is organized into spatially confined sub-compartments in nucleus. However, accurately identifying from chromatin data remains a challenge computational biology. Here, we present Sub-Compartment Identifier (SCI), an algorithm that uses graph embedding followed by unsupervised learning to predict using Hi-C data. We find network topological centrality and clustering performance of SCI sub-compartment predictions are superior...
Enhancers are cis -acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification enhancers, coupled with comprehensive functional analysis their properties, could improve our understanding complex gene transcription mechanisms and regulation processes general. We developed DENdb, centralized on-line repository predicted enhancers derived from multiple human cell-lines. DENdb integrates by five different methods generating an enriched...
Abstract Motivation: Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional silencing is a common mechanism in cancer for expression of tumor suppressor genes. Though several tools have been created to enable detection marks ChIP-seq data from normal samples, it unclear whether these can be efficiently applied generated samples. Indeed, genomes frequent copy number alterations: gains and losses large regions...
Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used methods TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, studies regulation eukaryotes frequently require numerous PWM models TFBSs due to a large number TFs involved. To overcome these problems we developed DRAF, novel method for that requires only 14 232 human TFs, while at same time significantly...
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information ncRNA across spectrum various cells/tissues. Here, we present FARNA, knowledgebase inferred 10,289 human transcripts (2,734 microRNA and 7,555 long ncRNA) 119 tissues 177 primary cells human. Since transcription factors (TFs) TF co-factors (TcoFs) crucial components regulatory machinery for...
Using the Cap Analysis of Gene Expression (CAGE) technology, FANTOM5 consortium provided one most comprehensive maps transcription start sites (TSSs) in several species. Strikingly, ~72% them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs show that, all species studied, significant fraction CAGE peaks microsatellites, also called short tandem repeats (STRs). To confirm this transcription,...
In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for within genomic sequences plants that correspond to TISs. Our requires only genome sequence, not expressed Its sensitivity/specificity is A.t. (90.75%/92.2%), Vitis vinifera (66.8%/94.4%) and Populus trichocarpa (81.6%/94.4%), which suggests our can be used...
Comparing histone modification profiles between cancer and normal states, or across different tumor samples, can provide insights into understanding initiation, progression response to therapy. ChIP-seq data of samples are distorted by copy number variation innate any cell. We present HMCan-diff, the first method designed analyze detect changes in modifications two genetic backgrounds, a sample control. HMCan-diff explicitly corrects for bias, other biases data, which significantly improves...
Identification of interactions drugs and proteins is an essential step in the early stages drug discovery finding new uses. Traditional experimental identification validation these are still time-consuming, expensive, do not have a high success rate. To improve this process, development computational methods to predict rank likely drug-target (DTI) with minimum error rate would be great help. In work, we propose method for (Drug-Target interaction prediction using Graph Embedding graph...
Intra-tumoral epigenetic heterogeneity is an indicator of tumor population fitness and linked to the deregulation transcription. However, there no published computational tool automate measurement intra-tumoral allelic heterogeneity. We developed R/Bioconductor package, epihet, calculate perform differential analysis. Furthermore, epihet can implement a biological network analysis workflow for transforming cancer-specific loci into cancer-related function clinical biomarkers. Finally, we...
Abstract In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance levels a spatiotemporal manner. One most challenging questions is how genomic characteristics relate to enhancer activities. To date, only limited number sequence have been investigated, leaving space for exploring enhancers’ DNA code more systematic way. address this problem, we developed novel computational framework, Transcribed Enhancer Landscape Search...
Abstract Objective The T1GER study showed that treatment with the TNFα inhibitor golimumab in recently diagnosed type 1 diabetes patients better preservation of endogenous insulin production than placebo. However, considerable variation was observed among subjects. Therefore, a range biomarkers were investigated for their potential to predict response golimumab. Research Design and Methods Baseline blood samples from 79 subjects tested autoantibodies, microRNA, metabolites, lipids,...
ABSTRACT In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance levels spatiotemporal manner. One most challenging questions biology today is how genomic characteristics relate to enhancer activities. This particularly critical, as several recent studies have linked sequence motifs specific functional roles. To date, only a limited number been investigated, leaving space for exploring code more systematic way. address this...