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Welcome to my BugSigDB Curation Portfolio! Here, I’m actively curating microbiome studies for the BugSigDB project and documenting each step, from extracting microbial signatures to interpreting study designs and standardizing taxa information.
This repository serves as:
- A portfolio of my microbiome curation work
- Documentation of my contributions to BugSigDB
- A reference for future microbiome-related projects
- Record of open-source contributions
I contribute by:
- Curating microbial signatures from published research articles
- Interpreting statistical outputs (LEfSe, Wilcoxon, Mann–Whitney, DESeq2, Random Forest, Poisson, ANOVA, Songbird analysis, SparCc, etc.)
- Identifying valid taxa using the NCBI Taxonomy Browser
- Applying BugSigDB curation rules to ensure consistency and accuracy
- Documenting study design, matching, confounders, and significant taxa
- Engaging in team-based collaboration
All curations follow the official BugSigDB curation policy.
- Gut Microbiota Composition in Pregnant Women with Preeclampsia, 2025
- Gut Microbiota in Children with Intoxication-Type Inborn Errors of Metabolism (IEMs), 2026
- Gut Microbiota and Aggressive Behavior in Working Dogs, 2025
- Gut Microbiota in Parkinson's Disease and Constipation-Predominant Irritable Bowel Syndrome, 2026
- Age Related Gut Microbiome and Links to Police Performance in Kunming Dogs, 2026
- Defining Microbial Biomarkers for Risk of Preterm Labor, 2020
- Semen Microbiota in Men with Abnormal Sperm Parameters, 2024
- Blood Bacterial 16S rRNA Gene Alterations in Women with Polycystic Ovary Syndrome (PCOS), 2022
- The Gut Microbiota Associated with High-Gleason Prostate Cancer
- Highly Specific Vaginal Microbiome Signature for Gynecological Cancers
- The Adenoids but Not the Palatine Tonsils Serve as a Reservoir for Bacteria Associated with Secretory Otitis Media in Small Children
- Differential Effects of Sulfur Amino Acid-Restricted and Low-Calorie Diets on Gut Microbiome Profile and Bile Acid Composition
- Main differential endometrial microbiota associated with recurrent implantation failure: a case control study
- Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women
- Unraveling the Dysbiosis of Vaginal Microbiome to Understand Cervical Cancer Disease Etiology-An Explainable AI Approach
- Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms
- Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye
- The gut microbiome and metabolome associate with Schistosoma mansoni infection and cardiovascular disease risk in Uganda
- High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome
- Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study
- Exploring the characteristics of gut microbiota in the development and progression of early-stage colorectal cancer based on metagenomic sequencing
- Aging characteristics of colorectal cancer based on gut microbiota
- Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database
- Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals
- Altered gut microbiome composition by appendectomy contributes to colorectal cancer
- Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography
- Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer
- Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer
- Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients
- Characterization of tongue coating microbiome from patients with colorectal cancer
- Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients
- Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index
- Profiling gut microbiota of colorectal cancer in Indonesia: a focus on beneficial taxa depletion
- Colorectal Cancer Patients Have Four Specific Bacterial Species in Oral and Gut Microbiota in Common-A Metagenomic Comparison with Healthy Subjects
- Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer
- Oral Microbiota Alterations and Potential Salivary Biomarkers in Colorectal Cancer: A Next-Generation Sequencing Study
- Metagenomic Signatures of Colorectal Cancer in the Jordanian Population: A Regional Case-Control Analysis Using 16S rRNA Profiling
- Alterations in co-abundant bacteriome in colorectal cancer and its persistence after surgery: a pilot study
- Differences in the On- and Off-Tumor Microbiota between Right- and Left-Sided Colorectal Cancer
- Effect of breast milk with or without bacteria on infant gut microbiota
- Association between vaginal microbiome alteration and povidone iodine use during delivery
- Gut microbiota signatures associated with lithium treatment and clinical response in patients with bipolar disorder
- An exercise-associated gut microbiota signature enhances endurance performance: A study combining a human cohort and a mice FMT model
- Long lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer
- Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing
- The gut microbiota in adults with cystic fibrosis compared to colorectal cancer
- A pilot study of gut mucosal and faecal microbiota in rectal cancer: associations with histological response and adverse events following preoperative chemoradiotherapy
- Gut microbiome of Moroccan colorectal cancer patients
- Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients
- Colon Cancer Microbiome Landscaping: Differences in Right- and Left-Sided Colon Cancer and a Tumor Microbiome-Ileal Microbiome Association
- Gut microbiota signatures and predictive model of KPS in advanced colorectal cancer patients
This portfolio reflects my interests in:
- Microbiome research
- Scientific data curation
- Bioinformatics
- Research reproducibility
- Open science
- Data analysis & visualization
- BugSigDB curation platform
- BugSigDB Curation Guide
- NCBI Taxonomy Browser
- Research article figures, tables, and supplementary files
- Statistical reasoning and study design evaluation
If you have questions about any curation, feel free to contact me: https://github.com/lightamadi-stack