Jeremy Adams
A5055119846- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Human Resource and Talent Management
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Diverticular Disease and Complications
- Pancreatic and Hepatic Oncology Research
- Evolution and Genetic Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Leadership, Behavior, and Decision-Making Studies
- Organizational Learning and Leadership
- Botulinum Toxin and Related Neurological Disorders
- Colorectal Cancer Screening and Detection
- Colorectal Cancer Treatments and Studies
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Genetic factors in colorectal cancer
- Ethics in Clinical Research
- Diphtheria, Corynebacterium, and Tetanus
- Streptococcal Infections and Treatments
Ontario Institute for Cancer Research
2020-2023
Digital Research Alliance of Canada
2021
Ontario Genomics
2021
University of Waterloo
2014-2016
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical genomic data through both harmonized aggregation federated approaches. decreasing cost sequencing (along with other genome-wide molecular assays) increasing evidence its utility will soon drive generation sequence from tens millions humans, levels diversity. In this perspective, we present GA4GH strategies addressing major challenges revolution. We...
Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional significantly mutated find that among hypermutated tumors, an increased mutation burden associated improved CRC-specific (HR = 0.42, 95% CI:...
Clostridial neurotoxins (CNTs) are the deadliest toxins known and causative agents of botulism tetanus. Despite their structural functional complexity, no CNT homologs currently outside Clostridium . Here, we report first CNTs within genome rice fermentation organism Weissella oryzae SG25. One gene in W. S25 encodes a protein with four‐domain architecture HExxH protease motif common to botulinum (BoNTs). An adjacent partial similarity is also present, both genes seem have been laterally...
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Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing.We have created refget, Global Alliance Genomics and Health API specification to access reference sub-sequences an identifier derived from the sequence itself. We present four implementations across in-house cloud infrastructure, compliance suite web report used ensure conformity implementations.The refget can be found at:...
Spatially clustered mutations within specific regions of protein structure are thought to result from strong positive selection for altered functions and a common feature oncoproteins in cancer. Although previous studies have used spatial substitution clustering identify between pairs proteins, the ability this approach functional shifts phylogenies has not been explored.We implemented measure (the P3D statistic) extended it detect spatially substitutions at branches phylogenetic trees. We...
Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API secure to in matrix form. RNAget provides slicing matrices extract desired subsets is applicable all expression matrix-format data, including RNA sequencing microarrays. Further, it generalizes other sequence-based genomics such as ATAC-seq ChIP-seq.https://ga4gh-rnaseq.github.io/schema/docs/index.html.
ABSTRACT Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, Global Alliance Genomics and Health API specification to access reference sub-sequences an identifier derived from the sequence itself. present four implementations across in-house cloud infrastructure, compliance suite web report used ensure conformity implementations. https://w3id.org/ga4gh/refget .