Pratik Jagtap NIH Biosketch

Profile name:: Pratik Jagtap NIH Biosketch
Profile type:: Old NIH BioSketch NIH Biographical Sketch Instructions (PDF)
Last Updated:: 8 January 2017

OMB No. 0925-0001 and 0925-0002 (Rev. 10/2021 Approved Through 01/31/2026)

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EDUCATION/TRAINING

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A. Personal Statement

As Research Assistant Professor at the University of Minnesota, my current research interest includes developing analytical workflows using Galaxy platform in the area of proteomics, especially in emerging area of metaproteomics, proteogenomics and data-independent acquisition (DIA). As part of the Galaxy-P team for last five years, I have presented multiple posters, oral presentations and workshops at the national annual conferences of ABRF, ASMS and GCC. Recently, in June 2016, we presented many posters, an oral presentation and a workshop at the ASMS Conference held in San Antonio. I also presented a talk and workshop at the Galaxy Community Conference in Bloomington in June 2016. In October 2015, I was the Editor for a special issue of PROTEOMICS on the topic of “Microbiomes”. I am also a member of the ABRF Proteomics Research Group (PRG) for year 2014-2018. From 2013-2016, in my role as Managing Director of the Center for Mass Spectrometry and Proteomics (CMSP), I was involved in day-to-day activities of CMSP at the University of Minnesota. This involved managing personnel for sample preparation, instrumentation, data analysis and business management. From July 2012 – September 2013, I was Minnesota Supercomputing Institute (MSI) project manager for proteomics related projects. Most notably for the Galaxy-P grant, we have utilized and published various search workflows for data analysis. This has resulted in building multi-step, shareable and versatile workflows within Galaxy-P for analysis of metaproteomics and proteogenomics projects. From October 2010 until July 2012, as a manager of Scientific Consulting Group at MSI, I managed a group of scientific consultants in disciplines ranging from bioinformatics, biostatistics, high performance computing, remote visualization, image processing, software management and lab management. Until 2008, at the University of Michigan, as a member of Proteomics Alliance for Cancer Research (PACR), I was involved in multiple projects along with prominent researchers in the field of proteomics and cancer research. I have collaborated with researchers, both within and outside the Institute and produced peer-reviewed publications. As a result, I am aware of the importance of timely and effective communication, especially in an inter-disciplinary and emerging field such as proteomics – in order to achieve goals of a project such as proposed in this grant. In my current position, I have been exposed to and utilized various open-source software and search workflows for data analysis. I have worked closely with developers at MSI and at other institutes to test and integrate proteomic software in a pipeline. We are currently working with developers to have data-independent analysis software tools and pipeline integrated into Galaxy-P platform.

As Research Assistant Professor at the University of Minnesota, my current research interest includes developing analytical workflows using Galaxy platform in the area of proteomics, especially in emerging area of metaproteomics, proteogenomics and data-independent acquisition (DIA). As part of the Galaxy-P team for last five years, I have presented multiple posters, oral presentations and workshops at the national annual conferences of ABRF, ASMS and GCC. Recently, in June 2016, we presented many posters, an oral presentation and a workshop at the ASMS Conference held in San Antonio. I also presented a talk and workshop at the Galaxy Community Conference in Bloomington in June 2016. In October 2015, I was the Editor for a special issue of PROTEOMICS on the topic of “Microbiomes”. I am also a member of the ABRF Proteomics Research Group (PRG) for year 2014-2018.
From 2013-2016, in my role as Managing Director of the Center for Mass Spectrometry and Proteomics (CMSP), I was involved in day-to-day activities of CMSP at the University of Minnesota. This involved managing personnel for sample preparation, instrumentation, data analysis and business management. 
From July 2012 – September 2013, I was Minnesota Supercomputing Institute (MSI) project manager for proteomics related projects. Most notably for the Galaxy-P grant, we have utilized and published various search workflows for data analysis. This has resulted in building multi-step, shareable and versatile workflows within Galaxy-P for analysis of metaproteomics and proteogenomics projects. From October 2010 until July 2012, as a manager of Scientific Consulting Group at MSI, I managed a group of scientific consultants in disciplines ranging from bioinformatics, biostatistics, high performance computing, remote visualization, image processing, software management and lab management. Until 2008, at the University of Michigan, as a member of Proteomics Alliance for Cancer Research (PACR), I was involved in multiple projects along with prominent researchers in the field of proteomics and cancer research. I have collaborated with researchers, both within and outside the Institute and produced peer-reviewed publications. As a result, I am aware of the importance of timely and effective communication, especially in an inter-disciplinary and emerging field such as proteomics – in order to achieve goals of a project such as proposed in this grant. In my current position, I have been exposed to and utilized various open-source software and search workflows for data analysis. I have worked closely with developers at MSI and at other institutes to test and integrate proteomic software in a pipeline. We are currently working with developers to have data-independent analysis software tools and pipeline integrated into Galaxy-P platform.

As Research Assistant Professor at the University of Minnesota, my current research interest includes developing analytical workflows using Galaxy platform in the area of proteomics, especially in emerging area of metaproteomics, proteogenomics and data-independent acquisition (DIA). As part of the Galaxy-P team for last five years, I have presented multiple posters, oral presentations and workshops at the national annual conferences of ABRF, ASMS and GCC. Recently, in June 2016, we presented many posters, an oral presentation and a workshop at the ASMS Conference held in San Antonio. I also presented a talk and workshop at the Galaxy Community Conference in Bloomington in June 2016. In October 2015, I was the Editor for a special issue of PROTEOMICS on the topic of “Microbiomes”. I am also a member of the ABRF Proteomics Research Group (PRG) for year 2014-2018. From 2013-2016, in my role as Managing Director of the Center for Mass Spectrometry and Proteomics (CMSP), I was involved in day-to-day activities of CMSP at the University of Minnesota. This involved managing personnel for sample preparation, instrumentation, data analysis and business management. From July 2012 – September 2013, I was Minnesota Supercomputing Institute (MSI) project manager for proteomics related projects. Most notably for the Galaxy-P grant, we have utilized and published various search workflows for data analysis. This has resulted in building multi-step, shareable and versatile workflows within Galaxy-P for analysis of metaproteomics and proteogenomics projects. From October 2010 until July 2012, as a manager of Scientific Consulting Group at MSI, I managed a group of scientific consultants in disciplines ranging from bioinformatics, biostatistics, high performance computing, remote visualization, image processing, software management and lab management. Until 2008, at the University of Michigan, as a member of Proteomics Alliance for Cancer Research (PACR), I was involved in multiple projects along with prominent researchers in the field of proteomics and cancer research. I have collaborated with researchers, both within and outside the Institute and produced peer-reviewed publications. As a result, I am aware of the importance of timely and effective communication, especially in an inter-disciplinary and emerging field such as proteomics – in order to achieve goals of a project such as proposed in this grant. In my current position, I have been exposed to and utilized various open-source software and search workflows for data analysis. I have worked closely with developers at MSI and at other institutes to test and integrate proteomic software in a pipeline. We are currently working with developers to have data-independent analysis software tools and pipeline integrated into Galaxy-P platform.

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Jagtap P, Griffin T, Armengaud J. Microbiomes - embracing complexity. Proteomics. 2015 Oct;15(20):3405-6. PubMed ID: 26468045.
Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Käll L, Lehtiö J, Lukasse P, Moerland PD, Griffin TJ. Multi-omic data analysis using Galaxy. Nat Biotechnol. 2015 Feb;33(2):137-9. PubMed ID: 25658277.
Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. 2014 Dec 5;13(12):5898-908. PubMed Central ID: PMC4261978.
Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, Seymour SL, Griffin TJ. A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics. 2013 Apr;13(8):1352-7. PubMed Central ID: PMC3633484.

B. Positions and Honors

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Honors

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C. Contribution to Science

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GENOMICS / POST-GENOMIC ANALYSIS: Publications in the early phase of my career, were focused on genomic and post-genomic analysis of bacterial organisms. As a post-doctoral researcher at Max-Planck Institute of Developmental Biology, I had developed sample preparation protocols and run two-dimensional electrophoresis gels for post-genomic analysis of bacteria whose genomes were sequenced at the Institute. As a researcher on a Human Frontier Science Program grant along with researchers in England and Japan. . I was involved in ideation, proposal and execution of the grant on Bdellovibrio membrane biology. Genomic and proteomic analysis of Wolinella succinogenes demonstrated the presence of haemolytic enzymes in the proteome which suggested that it was an emerging pathogen. Analysis of Bdellovibrio bacteriovorus (a bacterial predator) helped in identifying lack of amino acid biosynthesis apparatus for nine essential amino acids. Moreover, study of bacterial membrane proteins also helped in identification of outer membrane proteins involved in host-dependent and independent lifestyle of the bacterium.

GENOMICS / POST-GENOMIC ANALYSIS: 
Publications in the early phase of my career, were focused on genomic and post-genomic analysis of bacterial organisms. As a post-doctoral researcher at Max-Planck Institute of Developmental Biology, I had developed sample preparation protocols and run two-dimensional electrophoresis gels for post-genomic analysis of bacteria whose genomes were sequenced at the Institute. As a researcher on a Human Frontier Science Program grant along with researchers in England and Japan. . I was involved in ideation, proposal and execution of the grant on Bdellovibrio membrane biology.  Genomic and proteomic analysis of Wolinella succinogenes demonstrated the presence of haemolytic enzymes in the proteome which suggested that it was an emerging pathogen. Analysis of Bdellovibrio bacteriovorus (a bacterial predator) helped in identifying lack of amino acid biosynthesis apparatus for nine essential amino acids. Moreover, study of bacterial membrane proteins also helped in identification of outer membrane proteins involved in host-dependent and independent lifestyle of the bacterium.

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Citations

Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, Jagtap P, Linke B, Meyer F, Lederer H, Schuster SC. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11690-5. PubMed Central ID: PMC208819.
Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004 Jan 30;303(5658):689-92. PubMed ID: 14752164.
Janagama HK, Senthilkumar, Bannantine JP, Kugadas A, Jagtap P, Higgins L, Witthuhn B, Sreevatsan S. Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent. BMC Microbiol. 2010 Oct 22;10:268. PubMed Central ID: PMC2975660.
Chang CY, Hobley L, Till R, Capeness M, Kanna M, Burtt W, Jagtap P, Aizawa SI, Sockett RE. The Bdellovibrio bacteriovorus twin-arginine transport system has roles in predatory and prey-independent growth. Microbiology (Reading). 2011 Nov;157(Pt 11):3079-3093. PubMed ID: 21903758.

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QUANTITATIVE PROTEOMICS: At the University of Michigan, I worked on bacterial proteomics using iTRAQ labeling to study Bacillus anthracis germination, Bdellovibrio membrane protein expression and identification of temporal expression proteins during TGF-beta-Induced epithelial-mesenchymal transition (EMT). We identified multiple small acid soluble proteins (SASPs) that are degraded during germination. Some of these SASPs were not annotated in the strain under study and was an early proteogenomic study in temporal expression of SASPs. For the EMT study, we identified several proteins that were differentially expressed and could correlate it to mRNA expression of these genes.

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Citations

Jagtap P, Michailidis G, Zielke R, Walker AK, Patel N, Strahler JR, Driks A, Andrews PC, Maddock JR. Early events of Bacillus anthracis germination identified by time-course quantitative proteomics. Proteomics. 2006 Oct;6(19):5199-211. PubMed ID: 16927434.
Keshamouni VG, Jagtap P, Michailidis G, Strahler JR, Kuick R, Reka AK, Papoulias P, Krishnapuram R, Srirangam A, Standiford TJ, Andrews PC, Omenn GS. Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition. J Proteome Res. 2009 Jan;8(1):35-47. PubMed ID: 19118450; NIHMSID: NIHMS1606183.
Janagama HK, Senthilkumar, Bannantine JP, Kugadas A, Jagtap P, Higgins L, Witthuhn B, Sreevatsan S. Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent. BMC Microbiol. 2010 Oct 22;10:268. PubMed Central ID: PMC2975660.
Mahoney DW, Therneau TM, Heppelmann CJ, Higgins L, Benson LM, Zenka RM, Jagtap P, Nelsestuen GL, Bergen HR, Oberg AL. Relative quantification: characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ-labeled peptides. J Proteome Res. 2011 Sep 2;10(9):4325-33. PubMed Central ID: PMC3166364.

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METAPROTEOMICS: Recently, the research focus has been on method development and application of analytical workflows in the field of metaproteomics. The field presents a n analytical challenge mainly because of the large size of databases that are used for database searching. We have used a two-step method that has hence been used by other research groups to identify bacterial species present in saliva. We have also successfully implemented this method within Galaxy platform and these workflows are used in other metaproteomic analysis studies at the University of Minnesota.

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Citations

Rudney JD, Jagtap PD, Reilly CS, Chen R, Markowski TW, Higgins L, Johnson JE, Griffin TJ. Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries. Microbiome. 2015 Dec 19;3:69. PubMed Central ID: PMC4684605.
Jagtap P, Griffin T, Armengaud J. Microbiomes - embracing complexity. Proteomics. 2015 Oct;15(20):3405-6. PubMed ID: 26468045.
Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ. Metaproteomic analysis using the Galaxy framework. Proteomics. 2015 Oct;15(20):3553-65. PubMed ID: 26058579.
Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD. Deep metaproteomic analysis of human salivary supernatant. Proteomics. 2012 Apr;12(7):992-1001. PubMed Central ID: PMC3517020.

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PROTEOGENOMICS: We have developed analytical workflows within Galaxy platform that are used for proteogenomic analysis. These include an ‘abundance of caution’ at each filtering step so that only authentic proteoforms are reported. Our study on salivary dataset identified 52 novel proteoforms. Many of these proteoforms were identified in the Proline Rich Protein (PRP) gene coding region on chromosome 12. We have also developed workflows to generate protein FASTA database from RNASeq data. All the workflows are currently being used for multiple projects.

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Citations

Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype. J Proteome Res. 2016 Apr 1;15(4):1253-61. PubMed ID: 26903422.
Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics. J Proteome Res. 2015 Nov 6;14(11):4792-804. PubMed ID: 26435507.
Boekel J, Chilton JM, Cooke IR, Horvatovich PL, Jagtap PD, Käll L, Lehtiö J, Lukasse P, Moerland PD, Griffin TJ. Multi-omic data analysis using Galaxy. Nat Biotechnol. 2015 Feb;33(2):137-9. PubMed ID: 25658277.
Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Shenykman GM, Bandhakavi S, Smith LM, Griffin TJ. Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. 2014 Dec 5;13(12):5898-908. PubMed Central ID: PMC4261978.

D. Additional Information: Research Support and/or Scholastic Performance

Completed Research Support

1488103

2015/07/10-2018/08/31

1458524, National Science Foundation

Griffin (PI)

ABI Development: A unified Galaxy-based platform for multi-omic data analysis and informatics

The goals of the project are: 1) Enhance the Galaxy environment with new interactive visualization tools and data exchange functionalities necessary for effective multi-omic data analysis; 2) Extend the Galaxy environment to analyze and process diverse metabolomics data and support workflows for metabolic activity profiling; 3) Extend the Galaxy environment for integrative genomic-proteomic data analysis supporting proteogenomic and metaproteomic applications; 4) Ensure Broader Impact by promoting usage of Galaxy for multi-omics by the research community and providing undergraduate training opportunities in computational systems biology via a local area institutional network.

Role: Co-Investigator

1429937

2012/09/17-2017/06/30

5R01CA163864-03, National Institute of Health

Xing, Chengguo (PI)

Mechanisms of Anticancer Agents Selective against Drug Resistant Leukemia

The main objectives of this proposal are to elucidate the mechanisms of action for CXLs by employing the unique chemical probes and cancer models we developed and to validate its anticancer potential in a clinically relevant engraftment model.

Role: Co-Investigator

1532285

2016/05/01-2020/04/30

NIH U24 CA199347-01A1 (Griffin PI), National Institute of Health

Griffin, Tim (PI)

A Galaxy based multiomic informatics hub for cancer researchers

This application proposes to extend the Galaxy software framework to enable multi-omic data analysis for cancer research applications

Role: Co-Investigator

1429935

2012/07/15-2015/06/30

1147079, National Science Foundation

Timothy Griffin (PI)

ABI Development: Galaxy-P: A new community-based informatics paradigm for MS-based proteomics.

The major goal of this project is to integrate proteomics workflow using open source and commercial proteomics software into Galaxy analytical framework. My role in this project is management of analytical projects in the fields of proteogenomics, metaproteomics and quantitative proteomics.

Role: Co-Investigator