Senior Microbiome Research Scientist Resume Example Loma Linda University Medical Center

SENIOR MICROBIOME RESEARCH SCIENTIST

Professional Overview

Studious Senior Microbiome Research Scientist with 10 years of gut-microbiome research experience

Proven history of writing of publications, presentations, grants and reports

Strong working knowledge of R software

Currently advancing R knowledge with R programming by John Hopkins (coursera) and eager to learn new skills

Demonstrated experience with metagenomic (e.g. beta diversity) and metabolomic (e.g. IPA) data analysis

Proven expertise in multi-omic data integration with track record of publications in high impact journals

Possesses excellent time and project management skills to maintain freight quality and integrity

Proven excellence in research, communication and collaboration skills with publication record

Prior experience with analysis of human epidemiological research data

Determined to devote more effort to develop independent research

Extensive knowledge of gut-brain axis in neurological disease

Basic familiarity with scientific software management

Technical Skills and Qualifications

Prior experience with metagenomic and untargeted metabolomic data analysis

1. Yuan X, Long Y, Ji Z, Gao J, Fu T, Yan M, Zhang L, Su H, Zhang W, Wen X, Pu Z, Chen H, Wang Y, Gu X, Yan B, Kaliannan K, Shao Z. Green Tea Liquid Consumption Alters the Human Intestinal and Oral Microbiome. Mol Nutr Food Res. 2018 Jun; 62(12):e1800178. doi: 10.1002/mnfr.201800178. Epub 2018 Jun 10.

Corresponding author

2. Kaliannan K, Li XY, Wang B, Pan Q, Chen CY, Hao L, Xie S, Kang JX. Multi-omic analysis in transgenic mice implicates omega-6/omega-3 fatty acid imbalance as a risk factor for chronic disease. Commun Biol. 2019 Jul 26; 2:276. doi: 10.1038/s42003-019-0521-4. eCollection 2019.

3. Kaliannan K, Robertson RC, Murphy K, Stanton C, Kang C, Wang B, Hao L, Bhan AK, Kang JX. Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice. Microbiome. 2018 Nov 13;6(1):205. doi: 10.1186/s40168-018-0587-0.

4. Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C, Kang JX. Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota. Microbiome. 2018 May 24; 6(1):95. doi: 10.1186/s40168-018-0476-6.

5. Kang C, Wang B, Kaliannan K, Wang X, Lang H, Hui S, Huang L, Zhang Y, Zhou M, Chen M, Mi M. Gut Microbiota Mediates the Protective Effects of Dietary Capsaicin against Chronic Low-Grade Inflammation and Associated Obesity Induced by High-Fat Diet. MBio. 2017 May 23; 8(3). pii: e00470-17. doi: 10.1128/mBio.00470-17.

Strong working knowledge of R software

Currently advancing R knowledge with R programming by John Hopkins
https://www.coursera.org/learn/r-programming
Instructor 1: Roger D. Peng, PhD, Associate Professor, Biostatistics, Bloomberg School of Public Health
Instructor 2: Brian Caffo, PhD, Professor, Biostatistics, Bloomberg School of Public Health
Instructor 3: Jeff Leek, PhD, Associate Professor, Biostatistics, Bloomberg School of Public Health

Proven experience with grant preparation

Grant 1: "Early Detection of Obesity with Circulating Omega-6/Omega-3 Essential Fatty Acids Ratio"/The Global Grants for Gut Health (Yakult and Nature Research), 2019
Grant 2: "Non-Invasive Early Detection of Obesity With Fecal Intestinal Alkaline Phosphatase Levels"/Massachusetts General Hospital (MGH) Screening Technologies in Primary Care Innovation Fund (PCIF), 2019
Grant 3: Severity of SARS-CoV-2 infection in household contacts of patients with COVID-19: The role of epigenetics/Merck Investigator Studies Program (MISP): SARS CoV-2/COVID-19/2020
Grant 4: SARS-CoV-2 susceptibility and severity in essential workers and their children: The role of epigenetics/NIH RO1/2020
Grant 5: Whole-genome bisulfite sequencing of cell-free urinary DNA to improve the diagnosis of Urinary Tract infection in children/i4Kids Pilot Award 2020
Grant 6: IAP Regulating the Gut Flora: Implications for the Metabolic Syndrome/Nutrition Obesity Research Center at Harvard Medical School/2014
Grant 7: Preventative role of IAP in high fat diet induced metabolic syndrome/Ellison Foundation Award/Massachusetts General Hospital/2013
Grant 8: Treatment and Prevention of Metabolic Syndrome/ Partners Healthcare's 1st Annual Innovation Development Grant (IDG) program /2013

Adept at statistical analysis of metagenomics data

Community profiling/Visual exploration
Clustering &Correlation/Comparison &Classification
Functional profiling/Biomarker analysis/Biomarker meta-analysis
Alpha diversity (richness, evenness, observed taxa, rarefaction curve)
Phylogenetic tree and Heat tree
Beta diversity (weighted and unweighted UNIFRAC/Bray-Curtis/Jaccard/Jenson-Shannon distance methods)
PERMANOVA/ADONIS/PERMDISP
PCA/PCOA/nMDS/PLS-DA/RDA
Dendrogram analysis
Differential expression (zero-inflated Gaussian model/FitFeature model)
Differential expression (edgeR/DESeq2)
Heat-map analysis with hierarchical clustering
Core microbiome analysis
Predicted functional analysis (PICRUSt/Tax4Fun)
KEGG pathway analysis
Joint pathway analysis
Host-microbiome, microbe-microbe and microbe-metabolite interaction analysis (SparCC/MFA/CCA/RDA/PLS-DA/PLR-R)
Network visual analytics using modern software (e.g. Cytoscape)
Shotgun (bacteria/virus/fungi/antibiotic resistance/microbiome functions and pathways)
Biomarker analysis (e.g. LEfSe) and validation using machine learning (e.g. random forest) approach
Expertise working with several microbiome data analyzing software
PAST/XLSTAT-R/MicrobiomeAnalyst-R/MetaboAnalyst/IPA/SIMCA-P
https://huttenhower.sph.harvard.edu/galaxy/
Adept at bioinformatic analysis of shotgun metagenomic data (MetaPhlAn2/HUMAnN2/StrainPhlAn)
MaAsLin: Multivariate Analysis by Linear Models
Generalized Procrustes Analysis
Visually exploring metagenomic data with public data in 3D PCoA plot
Partial Least Squares Path Modeling/Structural Equation Modeling (SEM) using XLSTAT-R software
Testing causality through examination of both direct and indirect effects of bacteria on disease

Adept at statistical analysis of untargeted metabolomics data

Univariate Analysis
Fold Change Analysis
T-tests
Volcano plot
One-way Analysis of Variance (ANOVA)
Correlation Analysis
Pattern Searching
Chemometrics Analysis
Principal Component Analysis (PCA)
Partial Least Squares - Discriminant Analysis (PLS-DA)
Sparse Partial Least Squares - Discriminant Analysis (sPLS-DA)
Orthogonal Partial Least Squares - Discriminant Analysis (orthoPLS-DA)
Feature Identification
Significance Analysis of Microarray (and Metabolites) (SAM)
Empirical Bayesian Analysis of Microarray (and Metabolites) (EBAM)
Cluster Analysis
Hierarchical Clustering: Dendrogram/Heatmaps
Partitional Clustering: K-means/Self Organizing Map (SOM)
Classification & Feature Selection
Random Forest
Support Vector Machine (SVM)
Pathway analysis
Pathway Topology Analysis
Over Representation Analysis
Biomarker analysis
Classical univariate ROC curve analyses
Multivariate ROC curve based exploratory analysis (Explorer)
ROC curve-based model evaluation (Tester)
Enrichment analysis with network view

Prior experience with analysis of human epidemiological research data

1. Yuan X, Li X, Ji Z, Xiao J, Zhang L, Zhang W, Su H, Kaliannan K, Long Y, Shao Z. Effects of vitamin C supplementation on blood pressure and hypertension control in response to ambient temperature changes in patients with essential hypertension. Clin Exp Hypertens. 2019;41(5):414-421. doi: 10.1080/10641963.2018.1501056. Epub 2018 Sep 5.

2. Yuan X, Wang T, Gao J, Wang Y, Chen Y, Kaliannan K, Li X, Xiao J, Ma T, Zhang L, Shao Z. Associations of homocysteine status and homocysteine metabolism enzyme polymorphisms with hypertension and dyslipidemia in a Chinese hypertensive population. Clin Exp Hypertens. 2019 Feb 20:1-9. doi: 10.1080/10641963.2019.1571599. [Epub ahead of print].

Publications

Peer-Reviewed Scholarship in print or other media:

1. Kaliannan K, Li XY, Wang B, Pan Q, Chen CY, Hao L, Xie S, Kang JX. Multi-omic analysis in transgenic mice implicates omega-6/omega-3 fatty acid imbalance as a risk factor for chronic disease. Commun Biol. 2019 Jul 26; 2:276. doi: 10.1038/s42003-019-0521-4. eCollection 2019.

2. Kaliannan K, Robertson RC, Murphy K, Stanton C, Kang C, Wang B, Hao L, Bhan AK, Kang JX. Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice. Microbiome. 2018 Nov 13;6(1):205. doi: 10.1186/s40168-018-0587-0.

3. Kaliannan K, Hamarneh SR, Economopoulos KP, Nasrin Alam S, Moaven O, Patel P, Malo NS, Ray M, Abtahi SM, Muhammad N, Raychowdhury A, Teshager A, Mohamed MM, Moss AK, Ahmed R, Hakimian S, Narisawa S, Hohmann E, Warren HS, Bhan AK, Malo MS, Hodin RA. Intestinal alkaline phosphatase prevents metabolic syndrome in mice. Proc Natl Acad Sci USA. 2013 Apr 23; 110(17):7003-8. doi: 10.1073/pnas.1220180110. Epub 2013 Apr 8

4. Kaliannan K, Wang B, Li XY, Bhan AK, Kang JX. Omega-3 fatty acids prevent early-life antibiotic exposure-induced gut microbiota dysbiosis and later-life obesity. Int J Obes (Lond). 2016 Jun; 40(6):1039-42. doi: 10.1038/ijo.2016.27. Epub2016 Feb 15.

5. Kaliannan K, Wang B, Li XY, Kim KJ, Kang JX. A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci Rep. 2015 Jun 11; 5:11276. doi: 10.1038/srep11276.

6. Yuan X, Long Y, Ji Z, Gao J, Fu T, Yan M, Zhang L, Su H, Zhang W, Wen X, Pu Z, Chen H, Wang Y, Gu X, Yan B, Kaliannan K, Shao Z. Green Tea Liquid Consumption Alters the Human Intestinal and Oral Microbiome. Mol Nutr Food Res. 2018 Jun; 62(12):e1800178. doi: 10.1002/mnfr.201800178. Epub 2018 Jun 10.

7. Robertson RC, Kaliannan K, Strain CR, Ross RP, Stanton C, Kang JX. Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota. Microbiome

. 2018 May 24; 6(1):95. doi: 10.1186/s40168-018-0476-6.

8. Kang C, Wang B, Kaliannan K, Wang X, Lang H, Hui S, Huang L, Zhang Y, Zhou M, Chen M, Mi M. Gut Microbiota Mediates the Protective Effects of Dietary Capsaicin against Chronic Low-Grade Inflammation and Associated Obesity Induced by High-Fat Diet. MBio. 2017 May 23; 8(3). pii: e00470-17. doi: 10.1128/mBio.00470-17.

9. Economopoulos KP, Ward NL, Phillips CD, Teshager A, Patel P, Mohamed MM, Hakimian S, Cox SB, Ahmed R, Moaven O, Kaliannan K, Alam SN, Haller JF, Goldstein AM, Bhan AK, Malo MS, Hodin RA. Prevention of antibiotic associated metabolic syndrome in mice by intestinal alkaline phosphatase. Diabetes Obes Metab. 2016 May; 18(5):519-27. doi: 10.1111/dom.12645. Epub 2016 Mar 22.

10. Hamarneh SR, Mohamed MM, Economopoulos KP, Morrison SA, Phupitakphol T, Tantillo TJ, Gul SS, Gharedaghi MH, Tao Q, Kaliannan K, Narisawa S, Millan JL, van der Wilden GM, Fagenholz PJ, Malo MS, Hodin RA. A novel approach to maintain gut mucosal integrity using an oral enzyme supplement. Ann Surg. 2014 Oct; 260(4):706-14; discussion 714-5. doi: 10.1097/SLA.0000000000000916.

11. Hamarneh SR, Kim BM, Kaliannan K, Morrison SA, Tantillo TJ, Tao Q, Mohamed MMR, Ramirez JM, Karas A, Liu W, Hu D, Teshager A, Gul SS, Economopoulos KP, Bhan AK, Malo MS, Choi MY, Hodin RA. Intestinal Alkaline Phosphatase Attenuates Alcohol-Induced Hepatosteatosis in Mice. Dig Dis Sci. 2017 Apr 19. doi: 10.1007/s10620-017-4576-0. [Epub ahead of print].

12. Alam SN, Yammine H, Moaven O, Ahmed R, Moss AK, Biswas B, Muhammad N, Biswas R, Raychowdhury A, Kaliannan K, Ghosh S, Ray M, Hamarneh SR, Barua S, Malo NS, Bhan AK, Malo MS, Hodin RA. Intestinal alkaline phosphatase prevents antibiotic-induced susceptibility to enteric pathogens. Ann Surg. 2014 Apr; 259(4):715-22. doi: 10.1097/SLA.0b013e31828fae14.

13. Zubajlo RE, Benjamin A, Grajo JR, Kaliannan K, Kang JX, Bhan AK, Thomenius KE, Anthony BW, Dhyani M, Samir AE. Experimental Validation of Longitudinal Speed of Sound Estimates in the Diagnosis of Hepatic Steatosis (Part II). Ultrasound Med Biol. 2018 Dec;44(12):2749-2758. doi: 10.1016/j.ultrasmedbio.2018.07.020. Epub 2018 Sep 26.

14. Benjamin A, Zubajlo R, Thomenius K, Dhyani M, Kaliannan K, Samir AE, Anthony BW. Non-invasive diagnosis of non-alcoholic fatty liver disease (NAFLD) using ultrasound image echogenicity. Conf Proc IEEE Eng Med Biol Soc. 2017 Jul; 2017:2920-2923. doi: 10.1109/EMBC.2017.8037468.

15. Yuan X, Li X, Ji Z, Xiao J, Zhang L, Zhang W, Su H, Kaliannan K, Long Y, Shao Z. Effects of vitamin C supplementation on blood pressure and hypertension control in response to ambient temperature changes in patients with essential hypertension. Clin Exp Hypertens. 2019;41(5):414-421. doi: 10.1080/10641963.2018.1501056. Epub 2018 Sep 5.

16. Yuan X, Wang T, Gao J, Wang Y, Chen Y, Kaliannan K, Li X, Xiao J, Ma T, Zhang L, Shao Z. Associations of homocysteine status and homocysteine metabolism enzyme polymorphisms with hypertension and dyslipidemia in a Chinese hypertensive population. Clin Exp Hypertens. 2019 Feb 20:1-9. doi: 10.1080/10641963.2019.1571599. [Epub ahead of print].

17. Ramasamy S, Nguyen DD, Eston MA, Alam SN, Moss AK, Ebrahimi F, Biswas B, Mostafa G, Chen KT, Kaliannan K, Yammine H, Narisawa S, Millan JL, Warren HS, Hohmann EL, Mizoguchi E, Reinecker HC, Bhan AK, Snapper SB, Malo MS, Hodin RA. Intestinal alkaline phosphatase has beneficial effects in mouse models of chronic colitis. Inflamm Bowel Dis. 2011 Feb; 17(2):532-42. doi: 10.1002/ibd.21377.

18. Moss AK, Hamarneh SR, Mohamed MM, Ramasamy S, Yammine H, Patel P, Kaliannan K, Alam SN, Muhammad N, Moaven O, Teshager A, Malo NS, Narisawa S, Millan JL, Warren HS, Hohmann E, Malo MS, Hodin RA. Intestinal alkaline phosphatase inhibits the proinflammatory nucleotide uridine diphosphate. Am J Physiol Gastrointest Liver Physiol. 2013 Mar 15; 304(6): G597-604. doi:10.1152/ajpgi.00455.2012. Epub 2013 Jan 10.

19. Jagannath Malo. Jahangir Alam, Nondita S. Malo, Munjareen Shahnaz, Kanakaraju Kaliannan, Gopal Chandra, Tarek Aziz, Tapas Sarker, Mihir Bala, Ratna Paul, Chandan K. Saha, Pradip K. Karmakar, Madhu S. Malo. Intestinal Alkaline Phosphatase Deficiency Is Associated with Ischemic Heart Disease. Disease Markers. Volume 2019, Article ID 8473565, 11 pages. https://doi.org/10.1155/2019/8473565.

20. Liu K1, Hui S, Wang B, Kaliannan K, Guo X, Liang L. Comparative effects of different types of tree nut consumption on blood lipids: a network meta-analysis of clinical trials. Am J Clin Nutr. 2019 Nov 27. pii: nqz280. doi: 10.1093/ajcn/nqz280. [Epub ahead of print]

21. Cummings BM, Kaliannan K, Yager PH, Noviski N. Effect of Transition From a Unit-Based Team to External Transport Team for a Pediatric Critical Care Unit. J Intensive Care Med. 2016 Aug 10. pii: 0885066616662815. [Epub ahead of print].

Research publications without named authorship:

Kang C, Zhang Y, Zhu X, Liu K, Wang X, Chen M, Wang J, Chen H, Hui S, Huang L, Zhang Q, Zhu J, Wang B, Mi M. Healthy Subjects Differentially Respond to Dietary Capsaicin Correlating with Specific Gut Enterotypes. J Clin Endocrinol Metab. 2016 Dec;101(12):4681-4689. Epub 2016 Sep 27.

Non-peer Reviewed Scholarship in print or other media:

Kaliannan K. Compromise of α-Defensin Function in Liver Cirrhosis Facilitates the Toxic Relationship Between Gut Permeability and Endotoxemia. Dig Dis Sci. 2018 Oct;63(10):2492-2494. doi: 10.1007/s10620-018-5197-y.

Presentations

Oral presentations

Local:

Year/ Title of presentation/Department and Institution where presented

2011/The Effects of Orally Administered Intestinal Alkaline Phosphatase on High Fat Diet-Induced Metabolic Disorders/MGH Annual Research Progress meeting/Department of Surgery (Gastrointestinal unit), MGH
2011/Vagus Nerve Stimulators/Pediatric Critical Care Unit, Massachusetts General Hospital
2015/Omega-3 fatty acids prevent early-life antibiotic exposure-induced gut microbiota dysbiosis and later-life obesity/Harvard Catalyst Child Health Symposium: Developmental Origins of Health and Disease/Harvard Medical School, Boston, MA
2016/Elevated tissue omega-6 fatty acids alter gut microbiota and metabolome with increased chronic low-grade inflammation in fat-2 transgenic mice/Elevate your science symposium/Massachusetts General Hospital
2017/Omega-3 in Health Promotion and Disease Management: From Animal to Human/Inaugural Symposium of the International Society for Omega-3 Research (ISOR) Massachusetts General Hospital
2018/Gut microbiome mediates sex differences in metabolic syndrome in mice/Scientific Advisory Committee/Massachusetts General Hospital, Boston, MA
2018/Multi-omic analysis in transgenic mice implicates omega-6/omega-3 fatty acid imbalance as a risk factor for chronic disease/Massachusetts General Hospital Research Institute science slam/Cambridge Science Festival
2018/Integrated multi-omic analysis of unique transgenic animal models uncovers the tissue omega-6/omega-3 fatty acid imbalance as a critical risk factor for chronic disease/24th Functional Food Center conference Harvard Medical School, Boston, MA.

Regional:

2013/Intestinal Alkaline Phosphatase Prevents Acute Alcohol-Induced Liver Injury/The New England Surgical Society Annual Surgical Resident and Fellow Research Presentation Day/Hartford, Connecticut
2017/Discovering Microbiome-Related Nutritional Biomarkers for Chronic Diseases Using Multi-Omics and Transgenic Model Technologies/Cambridge Healthtech Institute's 3rd Annual Targeting the Microbiome/Boston, MA
2018/Gut microbiome mediates sex differences in metabolic syndrome in mice/Cambridge Healthtech Institute's 4th Annual Targeting the Microbiome Boston, MA
2019/Multi-Omic Analysis of Host-Microbiota Interactions Reveals the Synergetic Effects of Elevated Tissue Omega-3 Fatty Acids and Genistein supplementation on High-fat Diet Induced Obesity and Metabolic Syndrome/26th Functional Food Center conference San Diego, CA, USA
2020/ The Effects of Polyunsaturated Fatty Acids on the Gut Microbiome/Rhode Island Microbiome Symposium/January 17 at Avedisian Hall at the University of Rhode Island

National:

2012/The Effects of Orally Administered Intestinal Alkaline Phosphatase on High Fat Diet-Induced Metabolic Disorders/Digestive Disease Week (DDW) 2012/San Diego, California (American Gastroenterological Association)
2013/Intestinal Alkaline Phosphatase Prevents Acute Alcohol-Induced Liver Injury/Academic Surgical Congress (ASC) Scientific Program Committee/Orlando, Florida

International:

2014/Elevated tissue omega-3 fatty acid status prevents chronic low-grade inflammation by altering gut microbiota/11th Congress of the International Society for the Study of Fatty Acids and Lipids (ISSFAL)/Stockholm, Sweden
2015/A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia and chronic low-grade inflammation/12th World Congress on Inflammation/Boston, Massachusetts
2016/Dietary fat issues in current nutritional guidelines/Advances in Clinical Nutrition/Changzheng Hospital, Pudong, Shanghai, China
2016/A Host-Microbiome Interaction Mediates the Opposing Effects of Omega-6 and Omega-3 Fatty Acids on Metabolic Endotoxemia/International Conference on Omega-3 and Human Health (ICOHH)/Shanghai, China

Poster presentations

1. ATP-Induced Activation of NLRP3 Inflammasome and IL-1β Secretion Prevented by Intestinal Alkaline Phosphatase

Digestive Disease Week (DDW), 2011, American Gasteroenterological Association (AGA) institute
Awarded ‘Posters of distinction'

2. The Effects of Orally Administered Intestinal Alkaline Phosphatase on High-Fat Diet-Induced Metabolic Disorders.

Digestive Disease Week (DDW), 2012, AGA institute
Awarded ‘Posters of distinction'

3. Prevention Of Antibiotic-Associated Obesity In Mice By Intestinal Alkaline Phosphatase.

Academic Surgical Congress (ASC) Scientific Program, 2013
NESS Annual Surgical Resident and Fellow Research Presentation Day, 2013
Scientific Advisory Committee (SAC), 2013, Massachusetts General Hospital
Awarded ‘Posters of Merit'

4. Prevention of Fructose-Induced Obesity by Intestinal Alkaline Phosphatase.

Digestive Disease Week (DDW), 2013, American Gasteroenterological Association (AGA) institute
Scientific Advisory Committee (SAC), 2014, Massachusetts General Hospital

5. Intestinal Alkaline Phosphatase Is an Endogenous Anti-Inflammatory Factor.

Scientific Advisory Committee (SAC), 2013, Massachusetts General Hospital
Academic Surgical Congress (ASC) Scientific Program, 2013
NESS Annual Surgical Resident and Fellow Research Presentation Day, 2013

6. Transgenic mice convert carbohydrates to essential fatty acids: Implications for modern health epidemics.

11th Congress of the International Society for the Study of Fatty Acids and Lipids (ISSFAL), 2014. Stockholm, Sweden

7. Elevated tissue omega-6 fatty acids alter gut microbiota and metabolome with increased chronic low-grade inflammation in fat-2 transgenic mice.

Gut Health, Microbiota & Probiotics Throughout the Lifespan: Metabolic & Brain Function, 2016, Harvard Medical School
'6th Annual Obesity Research Incubator Session, 2017, The Cardiovascular, Diabetes & Metabolic Disorders (CVDM) Research Center, Brigham & Women's Research Institute, Boston, MA
MGH Research Fellow Poster Celebration, 2017
Awarded ‘Poster of Excellence'

8. Non-Invasive Diagnosis of Non-Alcoholic Fatty Liver Disease (NAFLD) using Ultrasound Image Echogenicity.

39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2017, Jeju Island, Korea

9. Gut microbiome mediates sex differences in the obesity and metabolic syndrome in mice.

“Gut Health, Microbiota & Probiotics Throughout the Lifespan 2018: Dietary Influences, Harvard Medical School, Boston, MA
MGH Research Fellow Poster Celebration, 2018 (selected finalist for posters of distinction award)
5th Annual Translational Microbiome Conference 2018, Boston, MA

10. Integrated metagenomic and metabolomic investigation of host-microbiota interactions reveals the beneficial effects of combination of elevated tissue omega-3 fatty acids and genistein supplementation on high-fat diet induced obesity and metabolic syndrome.

Scientific Advisory Committee (SAC), 2019, Massachusetts General Hospital, Boston, MA

Work Experience

Senior Microbiome Research Scientist03/2020 to CurrentLoma Linda University Medical CenterSan Bernardino , CA

Playing major role in supervising and performing laboratory experiments and on project planning, experimental design, data management, data analysis/interpretation, and manuscript/grant preparation
Overseeing laboratory projects and develops processes and procedures aligned with intended research outcomes
Genomic DNA and RNA extraction from urine and nasopharyngeal swab samples
PCR and RT PCR
Bacterial cultures, pathogen isolation, and sub-culturing
Performing ELISA and multiplex immunoassay
Microbial aseptic technique and culturing
Preserving samples
Recordkeeping, data analysis (R, python, etc.)
Collaborated with ZYMO Research for whole genome shotgun metagenomics
Analyzing children urine and upper airway 16S/Shotgun metagenomic microbiome data (Bacteria, Viruses, Fungi, Archaea and antibiotic resistance genes)
Analyzing children urine and upper airway whole transcriptomics data
Drafting 2 microbiome-based manuscripts for publication
Planning urine untargeted metabolomics with Pitt Health Sciences Metabolomics and Lipidomics Core
Planning urine whole genome bisulfite sequencing
Planning upper airway DNA methylation for COVID-19 studies
Planning upper airway whole transcriptomics for COVID-19 studies
Arranging EndNote libraries using EndNote X9
Conceived 3 new ideas and contributed as key personnel in 3 recently submitted grants
Established new collaborations to initiate contact tracing and surveillance-based COVID-19 research projects
Performing MALDI-TOF for bacterial identification
Performing calculations, tabulating, and statistically manipulating data and noting abnormalities and discrepancies
Maintaining lab database
Purchasing lab and research materials
Supervising and teaching technicians
Overseeing general lab coordinators, and maintenance, while interfacing with the clinical team
Organizing to maintain flow of testing area and providing continuous and efficient turnaround of specimens
Supervising work of research assistants in the laboratory

Instructor11/2017 to CurrentUniversity Of Massachusetts AmherstAmherst , MA

Achievements/Tasks

Collaborated with Dr. Zhongcong Xie (The Geriatric Anesthesia Research Unit at MGH) and analyzed fecal metagenomic and short-chain fatty acids (SCFA) data of Alzheimer's disease patients
Payed major role in laboratory and other research supervisory and training responsibilities
Involved in formal teaching of research fellows
Mentored trainees and faculty
Conducted weekly lab meetings
Developed unique FAT-2/FAT-1/FAT-1+2 transgenic mouse models
Investigated host-gut microbiota-metabolite axis using 16s rRNA sequencing and metabolomics in context of inflammatory disease
Discovered metabolic fingerprints and disease-pathway relevant biomarkers by integrated multi-omic data analysis
Published break-through research article in microbiome research field
Successfully applied grants based on identification of translational biomarkers
Grant 1: "Early Detection of Obesity with Circulating Omega-6/Omega-3 Essential Fatty Acids Ratio"/The Global Grants for Gut Health (Yakult and Nature Research), 2019
Grant 2: "Non-Invasive Early Detection of Obesity With Fecal Intestinal Alkaline Phosphatase Levels"/ Massachusetts General Hospital (MGH) Screening Technologies in Primary Care Innovation Fund (PCIF), 2019
Investigated effects of ''Kang's diet'' on cancer patients and analyzed gut microbiota and metabolomic data
Helped with designing clinical trials including cancer patients
Collected stool and blood
Measured plasma inflammatory markers using Luminex Cytokine Assay
Isolated genomic DNA from stool
Completed targeted microbiome analysis using q-PCR
Performed gut microbiome analysis using 16S gene sequencing
Performed metatranscriptome and metabolome analyses on blood samples
Investigated accuracy of ultrasound method invented by Massachusetts Institute of Technology (MIT)
Collaborated with Department of Radiology at Massachusetts General Hospital (MGH) and MIT
Received liver biopsy samples taken from patients with fatty liver disease
Tested enzymes expression using qPCR and immunoassay techniques
Investigated effects of fish oil on gut microbiota of type 2 diabetes patients
Collaborated with Medstar Shah Medical Group in Maryland, USA
Investigated effects of fish oil on inflammation and fecal microbiota
Designed double-blinded crossover randomized controlled Trial
Drafted Institutional Review Board (IRB) protocols

Research Fellow10/2012 to 10/2017Massachusetts General HospitalBrookline , MA

1. Extraction and purification of DNA from fecal samples

Extracted bacterial genomic DNA from fresh stool samples using QIAamp DNA Stool MiniKit
Determined DNA concentration and purity by Nanodrop spectrophotometer

2. Bacterial DNA measurement by 16S rRNA gene-based real-time quantitative PCR (qPCR)

Performed qPCR with PRISM 9000 Light Cycler using iTaquniversal SYBR Green Supermix and group specific primers
Determined specificity of the primers and limit of detection
Performed amplification program and data acquisition following protocol provided with SYBR Green
Generated standard curve using genomic DNA standard from reference bacterial strains (BEI Resources, Manassas, VA)
Determined 16S rRNA copy number by converting genomic standard quantities into genome copy numbers and then into 16S rRNA copy numbers
Expressed data as 16S rRNA gene copy number per gram of stool as well as relative abundance of percentage of total bacteria at sub-phylum level bacterial groups
Quantified short chain fatty acids (SCFA) producing fecal bacterial groups using qPCR
Quantified beta-glucuronidase producing bacterial groups using degenerate primers and qPCR
Isolated RNA from mice tissues, made complementary DNA and quantified expression of various genes using reverse-transcription qPCR

3. 16S rRNA sequencing

Performed 16s sequencing library preparation on DNA samples according to the Illumina 16S metagenomic sequencing library protocol
Amplified the V3-V4 region of the 16S rRNA gene using qPCR
Performed clean-up and purification of PCR product using Agencourt AMPure XP system
Performed second PCR reaction to incorporate a unique indexing primer pair to each sample
Performed quantification of samples using DNA quantification assay kit
Performed sequencing using Illumina MiSeq 2x300 bp paired end sequencing

4.Processing of 16S sequence data

Performed bioinformatic analysis of the sequence data with 64-bit version of USEARCH 8.1.1825 nd mother v.1.36.1

5. Analysis of 16S sequencing data using bioinformatics software

Performed data rarefying and scaling and transformation
Performed visual exploration (stacked bar/area plot, interactive pie chart, rarefaction curve, phylogenetic tree and heat tree)
Performed community profiling (alpha and beta diversity analyses, core microbiome analysis, heat-map clustering, dendrogram analysis, correlation network using SparCC and pattern search
Compared and classified bacterial groups (classical univariate analysis and differential abundance analysis using DESeq2 or edgeR algorithm)
Performed biomarker bacteria analysis (Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and Random Forest techniques)
Predicted functional potential of microbiota (PICRUSt)
Converted demultiplexed FASTA sequences into BIOM format using QIIME software
Aligned predicted genes and functions to KEGG database
Determined significant putative KEGG orthologs using STAMP software and shotgun data profiling (overall functional profiling, clustering analysis, differential abundance and biomarker analysis)
Performed inter-omic and host-microbiome interaction analyses (Performing different types of correlation analysis/constructing networks and visualizing it using Gephi software/PLS-DA and OPLS-DA and PLS-R modeling of data/CCA/RdA/MFA to find the causative link between dependent and explanatory variables)

6. Analysis of metabolomics data

Performed enrichment analysis and presented results in network and bar plot views
Performed pathway analysis
Performed PLS-DA and OPLS-DA statistical analyses
Performed integrated metabolic pathway analysis with 16S sequencing data (metabolite-gene and metabolite-metabolite and metabolite-disease and metabolite-gene-disease interaction networks)

4. Microbial aseptic technique and culturing

Prepared anaerobically sterilized non-selective, selective and differential media (e.g. Brucella blood agar, Bifido selective agar, Brain Heart Infusion Agar, Bacteroides Vulgatus Selective Agar, Bacteroides bile esculin agar Lactobacillus-MRS Agar, and Cooked meat media)
Cultured aerobic and obligate (e.g. Clostridium, Bacteroides and Bifidobacterium) and facultative (e.g. E. coli, Staphylococcus, Listeria and Lactobacillus) anaerobes
Created anaerobic environment using Bio-Bag™ Environmental Chambers and McIntosh and Filde's anaerobic jar
Isolated and identified different types of anaerobic bacteria
Studied metabolism (e.g. requirement of oxygen, need of CO2, capacity to form pigments)
Isolated in pure form (plating on solid culture media)
Identified them with staining reactions (simple, differential and special stains)
Identified them based on morphology of bacterial colony (shape, size, elevation, margin and surface) and cultural characteristics (color, texture and surface) and biochemical properties (e.g. indole test, lactose fermentation, methyl Red/Voges-Proskauer, citrate Utilization test) Conducted enzyme tests (catalase, urease, oxidase and nitrate) Experienced with key identification characteristics for Enterobacteriaceae (E. coli, Proteus and Salmonella)
Conducted global metabolite analysis and analyzed fecal and serum amino acid and SCFA in metabolic disease
Predicted amino acid and SCFA (butyrate, propionate, valerate and acetate) metabolism changes using 16S rRNA sequencing data and PICRUSt in metabolic disease context
Developed intestinal loop model in alive mice to study anaerobic bacterial growth
Acquired ampicillin-resistant Enterococcus and confirmed phenotype using biochemical test

5. Important achievements/tasks

Discovered opposing effects of omega-6 and omega-3 fats on gut microbiota using microbiological and molecular biological (qPCR) techniques
Utilized FAT-1 transgenic animal model to investigate host-microbiome interaction
Identified gut microbiota-based new mechanism of action for omega-3 fats
Identified pathway-based and biomarker-guided approach for nutritional intervention studies
Discovered preventive effects of omega-3 fats on early-life antibiotic exposure induced gut microbiota dysbiosis and later-life metabolic disease
Identified microbiome-based mechanism for sex-differences in metabolic disease and suggested novel therapeutic targets and strategies for management of metabolic disease
Produced 4 well-written and thoroughly vetted high-quality publications in high impact journals
Performed network analyses of microbiome and host metabolic phenotype interactions in the context of regulation of offspring obesity by maternal omega-3 fats
Established collaborations with other important scientists in field
Investigated effect of green tea liquid consumption on human microbiome (corresponding author)
Provided evidence green tea liquid consumption alters human oral and gut microbiome harmonious with anti-cancer activity
Identified preventive effects of omega-3 fats against anti-cancer drug-induced gut microbiome dysbiosis and toxicity
Performed Cox Proportional Hazard regression and estimated hazard ratios for association between baseline gut microbial enzyme and risk of CPT-11 drug-induced bloody diarrhea
Uncovered synergistic effects of omega-3 fat and isoflavones on gut microbiome and metabolic disease using 16s rRNA gene sequencing and metabolomics
Investigated preventive effects of omega-3 fats on alcohol + omega-6 rich food-induced alterations in gut microbiome-metabolite-immune axis related to liver disease
Investigated beneficial effects of dietary intervention on human gut microbiome and analyzed data using bioinformatics
Collaborated with Massachusetts Institute of Technology (MIT)and investigated accuracy of preclinical part of ultrasound method on fatty liver
Investigated association between stool biomarker and Ischemic Heart Disease
3 manuscripts and 2 review papers are in preparation
Presented data to internal and external audience
Received "Posters of Excellence" award
Performed hands-on laboratory work using cell-based assays, ELISA assays, flow cytometry, western blot, qPCR and RNA sequencing

Clinical Research Fellow10/2011 to 03/2012University Of MichiganAnn Arbor , MI

Investigated effects of transitioning unit-based transport team to external service on PICU
Conceptualized and designed study
Acquired data
Drafted manuscript
Accomplished one peer-reviewed publication
Investigated financial impact of out-of-pocket expenses on families with child admitted to Pediatric Critical Care Unit
Generated protocol for IRB submission
Generated new questionnaire
Interviewed parents of patients admitted to PICU
Acquired data
Drafted manuscript

Postdoctoral Research Fellow11/2009 to 09/2012Laboratory Of Gastrointestinal Epithelialogy, Massachusetts General Hospital, Harvard Medical SchoolCity , STATE

Achievements/Tasks

Learned molecular biology techniques (molecular cloning/RFLP/PCR/Gelelectrophoresis) and microbiological culture
Discovered novel preventive effects of gut enzyme (IAP) against metabolic disease resulted in seminal publication at high impact journal
Utilized IAP knockout mouse model to investigate mechanism of action of IAP in metabolic disease
Performed hands-on laboratory work using qPCR and ELISA and cell-based assays
Compared IAP levels between fasted and fed states in human ileal fluid samples
Conducted bacterial culture on ileal fluid samples
Demonstrated mastery of number of extraordinarily difficult techniques (e.g. Endotoxin measurement)
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
Generated award-winning abstracts
Won several awards and grants worth more than 350 million dollars (e.g. Ellison Foundation Award)
Presented well-written abstracts at scientific meetings
Presented data in weekly laboratory meetings
Investigated preventive effects of IAP against antibiotics, alcohol and high fructose induced metabolic disease
Investigated relationship between IAP and gut-barrier integrity
Changed primary focus of laboratory investigations to metabolic disease from inflammatory bowel disease

Editorial Activities

Ad hoc Reviewer

Digestive Diseases Sciences (DDS)
Molecular Nutrition and Food Research
Medical Hypothesis
Food research international
IJVSM
Clinical Medicine Insights: Gastroenterology
MicrobiologyOpen
Frontiers of Medicine
Endocrine, Metabolic & Immune Disorders - Drug Targets

Editor

International Journal of Gastroenterology
International Journal of Clinical Nutrition & Dietetics

Other Editorial Roles

'Lead Guest Editor', Mediators of Inflammation journal
Grand review activities: 2019/Harvard Catalyst Reactor Program, The Harvard Clinical and Translational Science Center/Reviewer for the Microbiome in Human Disease pilot grant

Education

Postdoctoral Research Fellowship: Postdoctoral Training2012Massachusetts General Hospital, Harvard Medical SchoolCity, USA

Bachelor of Medicine and Bachelor of Surgery: Medicine2008The Tamil Nadu Dr. M.G.R. Medical UniversityCity, State, India

Personal Information

Permanent resident (green card) of USA
Creative, highly motivated and flexible with work and shift hours
Committed, Humble, Dedicated and Accountable

Resume Overview

School Attended

Massachusetts General Hospital, Harvard Medical School
The Tamil Nadu Dr. M.G.R. Medical University

Job Titles Held:

Senior Microbiome Research Scientist
Instructor
Research Fellow
Clinical Research Fellow
Postdoctoral Research Fellow

Degrees

Postdoctoral Research Fellowship : Postdoctoral Training 2012
Bachelor of Medicine and Bachelor of Surgery : Medicine 2008

Senior Microbiome Research Scientist Resume Example

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