RNA/protein quantification, Nanodrop, Qubit, cDNA preparation, genotyping, library preparation for sequencing
Microscopy, Western blot, FISH, IHC, ELISA, Luminex
Terminal restriction fragment length polymorphism (TRFLP), Cloning using PCR and restriction enzymes,
Deep knowledge/strengths and weaknesses of individual omics technologies
Microbial phenotypic characterization, Aerobic and Anaerobic bacterial culturing using aseptic techniques, Culture media preparation, Optimization of media and fermentation conditions, Working with anaerobic workstations, Gram staining, Colony morphology, Cell morphology, Microbial assay of antibiotics, Microscopy, MALDI-TOF, Flow cytometry
FACS and biochemical ID (i.e., Vitek-MS), Lyophilization and freeze-drying of bacteria, Live/dead screening using bacterial viability kit, Bacterial counting, and enumeration
Bacterial endotoxin measurements using LAL assay, Viable titer (CFU), Bioactivity assays, ELISA, SDS-PAGE, Western blot, HPLC, Bioburden, Cross-immunity assays, Spectrum of Inhibition, Bacteriocin in silico Identification
Transformation and transfection assays, Serological testing, fluorescent in‐situ hybridization
1. Whole genome sequencing of bacterial genomes - tools and applications
2. Genomic Data Science: Algorithms for DNA Sequencing https://coursera.org/share/556d7045d9e7f1fe6b7d2c65916dae60
3. Data Science: Getting and Cleaning Data
4. Data Science: R Programming
5. Data Science: Advanced R Programming
6. Databases and SQL for Data Science
Senior Microbiome Research Scientist with 11 years of research experience related to impacts of diet on health through microbiome
11 years of nutritional science research experience (e.g., green tea/fish oil/high-fat diet/soy diet) related to gut microbiome with strong background in biochemistry/molecular biology/microbiology. Demonstrated expertise in conducting human clinical research on gut microbiome [e.g., green tea liquid consumption on gut microbiome (PubMed id: 29750437)] using specific meta-omics analysis coupled with innovative computational systems
Deep understanding of scientific methods (e.g., 16S rRNA sequencing/shotgun metagenomics/qPCR/metabolomics) used in gut microbiome research and bioinformatics pipelines/software/computational tools (e.g., QIIME/HUMAnN3/R/Galaxy) used in microbiome data analysis (e.g., microbial diversity/taxonomy/phylogenetic/functional analyses) as demonstrated in my track record of publications (e.g., Microbiome journal)
Proven expertise in integrative analysis of gut microbiome data with host metabolites data (e.g., Nature's Communications Biology journal) and host clinical parameters (e.g., Molecular Nutrition & Food Research journal) to translate results to business opportunities (e.g., Kang's diet for cancer patients)
Proven record of success in establishing external partnerships with global academic experts (e.g., Patrice D Cani, Belgium), scientific organizations (e.g., Research Center for Nutrition and Food Safety, China), and research institutes (e.g., APC Microbiome, Ireland), which increased lab efficiency
Demonstrated technical and scientific writing expertise and management/communication skills with track record for: (1) authoring over 20 manuscripts; (2) writing grants (e.g., NIH RO1) and protocols (e.g., standard operating procedures/data analysis pipeline); (3) managing teams to perform techniques (e.g., DNA/RNA isolation) and (4) communicating results to technical/non-technical audiences at meetings (e.g., Rhode Island Microbiome Symposium, 2020) and trade shows (e.g., Cambridge Healthtech Institute's Targeting the Microbiome, 2018)
Proven ability to: (1) manage complex projects (e.g., longitudinal analysis of human gut/oral or gut/urinary microbiome; integrated multi-omics analysis); (2) work with scientists having diverse cultural backgrounds/personalities/work styles and (3) communicate/work effectively in cross-functional (e.g., interdisciplinary research) and global teams (e.g., APC Microbiome, Ireland)
Senior Microbiome Research Scientist, 03/2020 to 09/2020 Pediatric Clinical and Translational Research Center, UPMC Children's Hospital of Pittsburgh - Pittsburgh, PA
Established and initiated running of new microbiome-based clinical research program (e.g., purchasing high-end instruments and arranging laboratory facilities/hiring technicians) at John G.
Research Center, communicated with members of “University of Pittsburgh Center for Medicine and the Microbiome” to establish new multi-disciplinary team and lead design and execution of pediatric clinical research studies.
Served as Subject Matter Expert for all aspects of microbiome sequencing research projects (gut microbiome/urinary and respiratory tracts microbiome), resulting in development of complex operational strategies and diverse molecular and bioinformatics tools to obtain and integrate microbiomic, metagenomic, and metatranscriptomic data with host epigenetic, transcriptomic and metabolomic data to investigate mechanisms of host-microbiome interactions in variety of pediatric health conditions.
Conceived/designed/executed new longitudinal, observational study in healthy infants to investigate association between gut microbiome and urinary tract microbiome and examine influence of demographic characteristics on early development of gut/urinary microbiome by performing shotgun metagenomic sequencing on serially collected stool and urine samples.
Wrote study design/sample collection protocols and experimental procedures/data analysis plan, reviewed/updated IRB protocol, prepared questionaries with inclusion/exclusion criteria and managed team.
Conceived and designed 5 different new studies using specific meta-omics and NGS technologies to utilize samples (stool/urine/nasopharyngeal) already collected from 4 different clinical trials and generate preliminary data for grants applications.
Constructed customized 16S data processing and analysis pipeline for lab.
Performed downstream bioinformatics analysis on stool/urine Illumina MiSeq 16S rRNA gene sequencing FASTQ data (Argonne National Laboratory) using QIIME2 pipeline (demultiplexing with cutadapt/read joining with vsearch/quality filtering/denoising with deblur/OTU clustering with vsearch/feature table construction and summaries), generated OTU table in BIOM format and phylogenetic tree file in NEWICK format using QIIME2-phylogeny plugin.
Performed alpha and beta diversity analysis with QIIME2-diversity plugin/alpha rarefaction plotting with QIIME2 diversity alpha-rarefaction visualizer/ taxonomic analysis with pre-trained Naive Bayes classifier and q2-feature-classifier plugin/differential abundance testing with ANCOM and Q2-composition plugin and paired sample (pre-ear infection and post-ear infection) comparisons with q2-longitudinal.
Predicted metagenome functional content from 16S marker gene by running PICRUSt1 pipeline to get KEGG ENZYME/KEGG orthologs and pathways and determined significant features using Linear discriminant analysis Effect Size (LEfSe) analysis.
Used hclust and randomForest R packages and LEfSe analysis on 16S data to perform hierarchical clustering and biomarker discovery.
Performed differential abundance analysis on 16S data using edgeR/DESeq2 and compared results with differential abundance results obtained from Zymo's shotgun metagenomic data.
Performed microbe-microbe interaction (co-occurrence and anti-occurrence) analysis using QIIME2-SCNIC (Sparse Cooccurrence Network Investigation for Compositional data) plugin.
Performed integrative transcriptome-metagenome analysis on stool/urine samples using mixOmics R package (N-integration with DIABLO) to explain molecular mechanism and impact of microbial variation on gene expression.
Performed integration of epigenetic data with host transcriptome data (quantitative trait loci-based integration) obtained from nasal samples using Matrix eQTL and SVA R packages.
Performed differential expression analysis on RNA-Sequencing data collected from nasal samples using edgeR/ DESeq2 to prepare preliminary data and figures for COVID-19 grant applications.
Solved issues/challenges (encountered by principal investigator in past) related to sample collection/transport/storage and wrote protocols and standardized experimental procedures to establish sample collection, transport, and preservation/DNA and RNA extraction and quantification methods by communicating with companies (e.g., ZYMO, Norgen, Argonne, COPAN, LONGHORN, Bio-Rad, VWR) and collaborating with UPMC genomic core facilities.
Conceived new study concept/designed (e.g., sequencing depth, coverage, how many biological or technical replicate) and identified right Illumina sequencing technique and library preparation methods for Dual RNA-Sequencing of urine samples to analyze both host/microbiomes simultaneously by communicating with “Health Sciences Sequencing Core” at UPMC (William A MacDonald, Ph.D.; http://www.nextgen.pitt.edu).
Designed and identified right sample collection/preparation methods for urine metabolomic study samples by communicating with director of Health Sciences Metabolomics and Lipidomics Core at UPMC (Stacy Gelhaus Wendell, Ph.D.; https://www.metabolomics.pitt.edu).
Communicated with Oxford Nanopore Technologies Inc.
(Stephanie Acosta) to set up the MinION Nanopore sequencing in lab, discuss IT/lab requirements and arrange “Rapid Start Day” onset training package to test ability of nanopore sequencing for rapid diagnosis of common pediatric infections.
Conceived new concept/designed study/prepared and shipped stool/urine samples for metatranscriptomics (gene activity diversity, gene expression abundance, and differential gene expression analysis) to compare abundance of expressed biological signatures with abundance of 16S general biological signatures.
Communicated with ‘CD Genomics' company to execute it.
Conceived new concept/designed study/prepared and shipped urine samples for Metagenomic Shotgun Sequencing (entire microbial composition and function/resistome and virulence profiles) using Illumina Nova-seq strategy to investigate ability of metagenomics for rapid and accurate diagnosis of urinary tract infections.
Communicated with ‘ZYMO' microbiomics company to execute this plan.
Conceived new concept/designed study to perform ‘microbial whole genome sequencing' on longitudinal nasal samples collected from ear infection trial to investigate association between microbial evolution and treatment failure.
Communicated with Dr.
Cooper, Vaughn Scott (Associate Director of University of Pittsburgh Center for Medicine and the Microbiome) to design this study.
Interviewed and Supervised 2 technicians/1 clinical research assistant to provide training, guidance, and advice on bench techniques (e.g., DNA/RNA isolation) and general laboratory practices.
Taught NGS technologies and their applications to PI to initiate new microbiome studies.
Wrote protocols and detailed plans/materials needed to perform stool/urine culture experiments.
Discussed with Department of Microbiology and Molecular Genetics (Jennifer Bomberger, Ph.D.) to initiate new collaboration for gut microbiome-focused COVID-19 grant.
Wrote 3 different pilot-study protocols (based on 2 DNA and 2 RNA extraction kits [Norgen and Zymo] /2 types of sample collection and storage buffers) for previously stored (fresh and freeze-thaw stool samples and urine samples stored at different time points) samples to standardize techniques and investigate quality of samples before utilizing them to metagenomic and transcriptomic analysis.
Learned and applied “CloudLIMS-based lab management” to manage biospecimens and metadata, locate stored samples, standardize operational workflows, and ensure sample integrity.
Conceived 4 new study concepts and grant proposals, deeply involved in writing (preliminary data development, hypothesis formulation, and grant narrative development), and submitting 3 COVID-19 grant applications in conjunction with PI for industry (Merck & Co) and NIH (RO1).
Participated in writing 1 manuscript that compared conventional urine culture with 16S sequencing for diagnosis of urinary tract infections.
Managed team to get right method/kits and perform cell-free DNA isolation from stool/urine samples to develop preliminary data for grants.
Established collaboration with Professor of Microbiology and Molecular Genetics (Cooper, Vaughn Scott) and independently wrote 1 whole-genome bisulfite sequencing (WGBS)-based university level grant worth $50,000.
Research Instructor, 11/2017 to 02/2020 Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital, Harvard Medical School - Boston, MA
Research Fellow, 10/2012 to 10/2017 Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital, Harvard Medical School - Boston, MA
Postdoctoral Research Fellow, 11/2009 to 09/2012 Laboratory of Gastrointestinal Epithelialogy, Massachusetts General Hospital, Harvard Medical School - Boston, MA
Learned commonly used molecular biology and microbiology techniques/traditional statistics and gained in-depth understanding of theories/principles underlying these methodologies by working with experienced molecular biologist and microbiome investigator.
Conceived/designed/executed 4 preclinical projects to investigate preventive/curative effects of intestinal alkaline phosphatase (IAP) on (1) high-fat diet-induced metabolic syndrome; (2) high-fructose-induced obesity and liver disease; (3) chronic-alcohol-induced liver disease and (4) early-life antibiotics and associated later-life obesity with high-fat diet, and role of IAP-mediated gut microbiome changes (bacterial stool culture/qPCR-based gut microbiota analysis) in these contexts.
Collaborated with molecular microbiologist (Sundaram Ramasamy.
Ph.D.) and performed DNA/RNA extraction and quantification from stool/tissue samples to investigate preventive effects of IAP supplementation and associated gut microbiota changes on inflammatory bowel disease (PMID: 20645323).
Worked with molecular biologist and performed terminal restriction fragment length polymorphism, phylogenetic analyses, and quantitative real-time PCR of subphylum-specific bacterial 16S rRNA genes to determine role of IAP on gut microbiota homeostasis.
Participated in 16S rRNA gene pyrosequencing to determine gut microbiome composition of antibiotics treated mice/processing and analysis of pyrosequencing data using “Research and Testing Laboratory's in-house pipeline” and vegan/ladbsv/DESeq2 R packages.
Collaborated with Research and Testing Laboratory, Texas, to perform 16S rRNA gene pyrosequencing and data analysis.
Established 3 new collaborations.
Developed, established, and validated standard procedures to measure bacterial endotoxin and markers of metabolic syndrome, bacterial translocation, and chronic inflammation.
Performed bacterial stool culture to investigate preventive effects of IAP supplementation against antibiotic-associated bacterial infections by preserving normal homeostasis of gut microbiota.
Collaborated with other members of lab and helped them in their experiments/compiled data and sent to lab supervisor and principal investigator/regularly presented data to weekly lab meeting/reviewed and improved 3 grant applications.
Won several awards and grants worth more than $400,000 (e.g., Ellison Foundation Award).
Presented well-written abstracts at scientific meetings (e.g., DDW by AGA).
Awarded posters of distinction and posters of merit.
Changed primary focus of laboratory investigations to metabolic disease from inflammatory bowel disease.
Translated preclinical findings with IAP to business opportunities to investigate role of IAP in patients with type 2 diabetes and ischemic heart disease and develop new IAP-based stool assay for early diagnosis.
M.D: : Medicine and Research, 03/2008The Tamil Nadu Dr. M.G.R. Medical University - Chennai, India
Higher Performance in Nutrition, Biochemistry, and Gastrointestinal System
Note: Complete list of publications/presentations will be due upon request
Human study 1: Collaborated with Chongqing Medical Nutrition Research Center in China, participated in study designing/data analysis/manuscript writing and discovered significant effects of gut enterotypes on beneficial effects of dietary capsaicin (chili powder) and new evidence for personalized nutrition guidance of capsaicin intervention on health promotion linking with gut microbiota patterns (PMID: 27676396).
Human study 2: Collected stool samples from centenarians living in Bama County, Guangxi, in China, performed 16S rRNA sequencing to analyze gut microbiome composition/function, and correlated results with their dietary omega-6 and omega-3 essential fatty acid levels.
Also, collected Betta-leaves they eat every day, worked with contract research organizations (International Chemistry Testing, Inc./Advanced Food Labs, Inc) to get results of microbiological/chemistry analyses, and performed preclinical studies to examine effects of betta-leaves on gut microbiome.
Human study 3: Collaborated with Department of Epidemiology, School of Public Health, Fourth Military Medical University, in China, performed data analysis and wrote manuscript to examine effects of vitamin C supplementation on blood pressure and hypertension control in response to ambient temperature changes in patients with essential hypertension.
Human study 4: Collaborated with Department of Epidemiology, School of Public Health, Fourth Military Medical University, in China, performed data analysis and wrote manuscript to examine associations of homocysteine status and homocysteine metabolism enzyme polymorphisms with hypertension and dyslipidemia in Chinese hypertensive population.
Human study 5: Collaborated with Research Center for Nutrition and Food Safety, Chongqing, in China, participated in network meta-analysis of randomized clinical trials aimed to assess comparative effects of walnuts, pistachios, hazelnuts, cashews, and almonds on typical lipid profiles, and wrote manuscript.
Human study 6: Collaborated with Chongqing Medical Nutrition Research Center in China (Chao Kang.
Ph.D.), wrote manuscript and performed data analysis using R packages to examine to investigate effect of exenatide, a glucagon-like peptide-1 receptor agonist, on kidney function/obesity indices/glucose control in overweight/obese patients with type 2 diabetes mellitus (under review in Nature's Nutrition & Diabetes journal).
Preclinical studies: Conceived/designed/executed/completed 7 new gut microbiome-based projects to investigate role of gut microbiome for (1) opposing effects of omega-6 and omega-3 fatty acids on chronic inflammatory disease; (2) preventing effects of omega-3 fatty acids on early life antibiotics and associated obesity in later life; (3) differences in liver disease associated with omega-6 fat +alcohol and omega-3 fat +alcohol combinations; (4) prevention of anti-cancer drug-induced gut toxicities with elevated omega-3 fatty acids; (5) sex-differences in obesity/metabolic syndrome; (6) combined effects of omega-3 fat and soy isoflavones on obesity/metabolic syndrome and (7) preventive effects of maternal omega-3 fatty acids during pregnancy/lactation on offspring obesity/metabolic diseases associated with high-fat diet.
Collaborated with Chongqing Medical Nutrition Research Center in China and participated in study designing/gut-microbiome data analysis/manuscript writing to investigate mediating role of gut microbiome for the anti-obesity effects of capsaicin (PMID: 27676396).
BIOINFORMATICS AND DATA ANALYSIS
1. Data Processing Tools for Next Generation Sequencing Data and Large Multi-Omic Datasets
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Companies Worked For:
Pediatric Clinical and Translational Research Center, UPMC Children's Hospital of Pittsburgh
Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital, Harvard Medical School
Laboratory of Gastrointestinal Epithelialogy, Massachusetts General Hospital, Harvard Medical School
The Tamil Nadu Dr. M.G.R. Medical University
Job Titles Held:
Senior Microbiome Research Scientist
Postdoctoral Research Fellow
M.D : : Medicine and Research , 03/2008 Higher Performance in Nutrition, Biochemistry, and Gastrointestinal System
Note: Complete list of publications/presentations will be due upon request
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