CV

Curriculum Vitae of Jeffrey L. Blanchard, Ph.D.

Updated: January 2019

 

EDUCATION

 

1990 - 1995 University of Georgia, Athens, GA, Ph.D., Botany

1984 - 1987 Worcester Polytechnic Institute, Worcester, MA, B.S., Biology - Honors

1981 - 1983 Vermont Technical College, Randolph, VT, A.E., Electrical Engineering - Honors

 

POSITIONS HELD

 

2014 - present Co-Director, UMass Center for Microbiome Research

2012 - present Associate Professor, Biology Department, UMass Amherst

2004 - present Member, Graduate Program in Molecular and Cellular Biology, UMass Amherst

2004 - present Member, Graduate Program in Organismal and Evolutionary Biology, UMass Amherst

2009 - 2012 Associate Professor, Department of Microbiology, UMass Amherst

2003 - 2009 Assistant Professor, Department of Microbiology, UMass Amherst

2002 - 2004 Adjunct Assistant Research Professor, Department of Molecular and Microbial Genetics, University of New Mexico, Albuquerque, NM

2000 - 2003 Research Scientist and Pathways Program Leader, National Center for Genome Resources, Santa Fe, NM

1998 - 1999 Postdoctoral Fellow, Promega Corporation, Madison, WI

1996 - 1998 Postdoctoral Fellow, Ecology and Evolution Group, University of Oregon, Eugene, OR

1990 - 1995 Graduate Research Associate, University of Georgia, Athens, GA

1987 - 1990 Laboratory Analyst, Genentech Inc., San Francisco, CA

 

RESEARCH

 

AWARDS

 

2017-2018 New England BioLabs Visiting Scholar (Guest room and laboratory costs)

2010 Harvard University Bullard Fellowship ($40,401)

 

GRANTS AND SUBCONTRACTS

 

2018-2021 Role: PI. Molecular responses to a short-term temperature toggle in a long-term soil warming experiment at Barre Woods. DOE Community Science Program. ~$80,000 in contributed costs

 

2018-2023 Role: Co-PI, Jonathan Thompson, Harvard University (PI). Harvard Forest LTER VI: From Microbes to Macrosystems: Understanding the response of ecological systems to global change drivers and their interactions. NSF. $5,000,000.

 

2017-2020 Role: Participant. Justin Fermann (PI). REU Site: Collaborative Undergraduate Research in Energy (CURE). NSF. $320,000

 

2017-2019* Role: PI. Raman-Spectroscopy and BONCAT Approaches for the Isolation and Identification of the Active Soil Community. DOE Community Science Program. ~$110,000 in contributed costs

 

2016-2019 Role: PI. Serita Frey, Marco Keiluweit, Jerry Melillo, Jackie Mohan, Jim Tang (Co-PIs). Response of the active forest soil community to long-term experimental warming. DOE Facilities Integrating Collaborations for User Science (FICUS) Program. ~$200,000 in contributed costs

 

2015-2020 Role: Participant. Aaron Ellison, Harvard University (PI). REU Site: Harvard Forest Summer Research Program in Forest Ecology: A forest full of Big Data. NSF. Total award $791,983

 

2014-2019 Role: Co-PI. Jerry Melillo, Marine Biological Laboratories (PI). LTREB: Soil warming and forest ecosystem feedbacks to the climate system. NSF. Total award $450,000

 

2014-2015 Role: PI. Collaborative Development of Protocols, Reagents, and Software for Metatranscriptomic and Epigenomic Research (with New England Biolabs). UMass Industry-Academic Research Grant Program. $25,000

 

2014-2015 Role: Co-PI, Beth McCormick, UMass Medical School (PI). Center for Microbiome Research. UMass President's Office Science & Technology Initiative Fund. $150,000

 

2014-2015 Role: PI. Probiotics for equine digestive health. UMass CVIP Technology Development Fund. $25,000

 

2014 Role: PI. National Ecological Observatory Network Workshop on Advanced Analysis of Genomic Data in Microbial Ecology Research. NSF. $50,00

 

2013-2015 Role: PI. I-Corp: Probiotics for the Prevention of Laminitis and Acidosis. NSF. $50,000

 

2013-2017 Role: Co-PI, Jerry Melillo, Marine Biological Laboratories (PI). Changes in Soil Carbon Dynamics in Response to Long-Term Soil Warming – Integration Across Scales from Cells to Ecosystems. DOE. $1,050,000

 

2013-2018 Role: Co-PI, David Foster, Harvard University (PI). Harvard Forest LTER V: New Science, Synthesis, Scholarship, and Strategic Vision for Society. NSF. $5,900,000

 

2013-2017 Role: Participant, Justin Ferman (PI). Collaborative Undergraduate Research in Energy Program. NSF. $300,000

 

2012-2017 Role: PI. Kristen DeAngelis, Serita Frey, Jerry Melillo, Linda van Diepen (Co-PIs). Microbial community dynamics in a long-term soil warming chronosequence. DOE Community Science Program. ~$220,000 in contributed costs

 

2012-2015 Role: Co-PI, Susan Leschine (PI). Enhancement of Feed Nutritional Value. Elanco Animal Health, $550,000

 

2012-2014 Role: Co-PI, Susan Leschine (PI). Understudied soil microbes with under appreciated capabilities: Untangling the Clostridium saccharolyticum group. DOE Community Sequencing Program. ~$80,000 in contributed costs

 

2012-2014 Role: PI. Synergistic catalysts for biofuel production from long term switchgrass microcosms. DOE Community Sequencing Program. ~$120,000 in contributed costs

 

2012-2013 Role: PI. Biofuel Production from Municipal Solid Waste. ReCommunity, $244,975

 

2011-2013 Role: Co-PI, Danny Schnell (PI). Development of a dedicated, high-value biofuels crop. DOE. $1,482,264

 

2011-2013 Role: Co-PI, Kristen DeAngelis (PI). Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils. DOE Community Sequencing Program. ~$100,000 in contributed costs

 

2011-2012 Role: Participant, David Foster, Harvard University (PI). Harvard Forest LTER IV: Integrated Studies of the Drivers, Dynamics, and Consequences of Landscape Change in New England. 6/2006 – 5/2012. $4,695,455

 

2010-2011 Role: PI. Novel genome-based approaches for understanding relationships between microbial forest soil community members. Harvard University Bullard Fellowship. $40,401 (direct/total)

 

2010-2015 Role: Co-PI, Kim Trembley (PI), Understanding liver bud emergence, formation and potential. NIH. $1,761,190

 

2010-2013 Role: Participant, Surita Bhatia (PI). REU Summer Site on Exploring Cellular Engineering and the Life Sciences (ExCELS). $328,766

 

2010-2011 Role: PI. Developing renewable alternatives to gasoline through experimental evolution. DOE Community Sequencing Program. $75,000 (In kind contribution).

 

2008-2011 Role: PI. Sustainable use of woody biomass as a renewable alternative to gasoline. USDA-CREES. $150,000

 

2008-2010 Role: Co-PI, John Fabel, Qteros (PI). Genome-enabled advancement of biomass to biofuel technology. DOE-SBIR Phase II. $130,000 (total award - $750,000).

 

2008-2009 Role: Consultant. SunEthanol (PI). A Novel Approach to Addressing Biomass Recalcitrance, Cellulose Crystallinity and Conversion Efficiency. DOE-SBIR Phase I $14,000 (total award - $100,000)

 

2008-2009 Role: PI. From Genomics to Human Health: A Novel Framework for Identifying Condition-Dependent Models of Apoptosis. Center for Apoptosis Research. $25,000.

 

2007-2012 Role: Participant. Susan Roberts (PI) IGERT: Interdisciplinary Research Training in Cellular Engineering. NSF. $2,403,240

 

2007-2008 Role: PI. Genome-based models of ethanol production in Clostridium phytofermentans. SRA with SunEthanol. $135,000

 

2007-2008 Role: Consultant, John Fabel, SunEthanol (PI). Genome-enabled advancement of biomass to biofuel technology. DOE-SBIR Phase I. $11,000 (total award - $100,000)

 

2007-2008 Role: Participant, Danny Schnell (PI), Elsbeth Walker (PI). Development of Brachypodium distachyon as a model system for the identification of optimal traits in plant cellulosic feedstocks for biofuels production. UMass NSM Energy Seed Grant. No direct funding. (total award - $35,000)

 

2007-2008 Role: participant, George Huber (PI). MRI-Acquisition of Instrumentation for a Biofuels Research Laboratory. NSF. No direct funding. (total award - $513,600)

 

2005-2006 Role: PI. The Reduction of Genomic and Regulatory Complexity in Marine Cyanobacteria. UMass Faculty Research Grant. $21,990

 

2005 Role: Collaborator, Peg Riley (PI). Genome Sequencing of Burkholderia phymatum STM815. Department of Energy. ~$100,000 In kind contribution

 

2005 Role: Collaborator, Susan Leschine (PI). Genome Sequencing of Clostridium phytofermentans. Department of Energy. ~$100,000 In kind contribution

 

2004-2009 Role: PI. Constructing graphical models of photosynthetic organisms from genomic data to detect climatically induced changes in cellular pathways. Massachusetts Agricultural Experiment Station Hatch Project. 2004-2009. $50,000

 

2003-2004 Role: Participant, Derek Lovely (PI). Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter. Department of Energy. $24,000 (total award - $5,000,000)

 

National Center for Genome Resources

 

2002-2004 Role: Subcontractor. The MIND Institute/University of New Mexico (PI). Molecular Markers of Cerebellar Dysfunction in Schizophrenia. $33,000

 

2002-2003 Role: Participant. Sandia National Laboratories (PI). Title: Carbon Sequestration of Synechococcus from Molecular to Hierarchical Modeling. $150,000 (total award - $19,000,000)

 

2002-2003 Role: Consultant. New Mexico State University (PI). NIH Biomedical Research Infrastructure Network. NIH. $5,000

 

2001-2002 Role: Subcontract. New Mexico State University (PI). Development of a Metabolic Pathways Database (PathDB) Army Research Organization. $191,000

 

 

Research Funding and Awards to Other Members of the Blanchard Research Group

2019-2020 Lionel Forbers, Life Sciences Junior Fellowship. $1,000

2019 Nadia L’Bahy, Commonwealth College Research Fellowship. $500

2018 Lauren Alteio, UMass Dissertation Fieldwork Grant. $3,000

2018 Lauren Alteio, Travel Award, $500

2018 William Rodriguez, Travel Award, $500

2018 Alex Truchon, Commonwealth College Research Fellowship. $500

2017-2018 Alex Truchon, Peter K. Hepler Research Scholarship. $2,000

2016-2017 Nick Mucci, Life Sciences Junior Fellowship Program, $2,000

2015-2016 Ava Bakhtyari, Commonwealth College Research Fellowship. ~$500

2015-2016 Madhura Kulkarni, Commonwealth College Research Fellowship. $1,000

2015-2016 Fauzia Iqbal, Commonwealth College Research Fellowship. ~$5000

2014-2015 Eric Gann, Commonwealth College Research Grant. $1,000

2014-2015 Ava Bakhtyari, Commonwealth College Research Fellowship. $1,000

2014-2015 Madhura Kulkarni, Commonwealth College Research Fellowship. $1,000

2014-2015 Shane Lawson, Commonwealth College Research Fellowship. $1,000

2014-2015 Fauzia Iqbal, Commonwealth College Research Fellowship. $1,000

2013-2014 William Rodriquez, Initiative for Maximizing Student Development. $23,000

2013-2014 Kelly Haas, NSF NEAGAP Fellowship, $23,000

2013-2014 Kelly Haas, UMass Graduate Research Grant. $1,000

2013-2014 Eric Gann, Commonwealth College Research Fellowship. $1,000

2012-2013 William Rodriquez, NIH Prep Fellowship, $23,000

2012-2013 Eric Gann, Commonwealth College Research Fellowship. $750

2012-2013 Amy Biddle, Morris Animal Foundation. $10,800

2010-2011 Tara Mahendrarajah, Life Sciences Junior Fellowship Program, $2,000

2011 Tara Mahendrarajah, Commonwealth College Research Fellowship. $450

2011-2012 Tara Mahendrarajah, Goldwater Scholarship, $7,500

2011-2013 Monique Tait, NSF Louis Stokes Fellowship, $50,000

2010-2011 Kelly Haas, NSF NEAGAP Fellowship, $22,000

2010 Caitlin Lauer, Commonwealth College Research Fellowship. $1,000

2010-2011 Stephen Godin, Life Sciences Junior Fellowship Program, $2,000

2010 Caitlin Lauer, HHMI Summer Internship. $4,100

2009-2010 Supratim Mukherjee, Isenberg Scholar Fellowship, $10,000

2009-2010 Monique Tait, NIH Prep Internship, $22,000

2009-2010 Danielle Amisano, Commonwealth College Research Fellowship. $1,000

2009-2010 Stephen Godin, Commonwealth College Research Grant. $1,000

2009 Stephen Godin, HHMI Summer Internship. $3,800

2008-2009 Stephen Godin, HHMI Academic Year Research Internship. $1,250

2008 Supratim Mukherjee, Institute of Cellular Engineering training grant. $2,000

2008 Zhiyi Sun, Travel Scholarship to NESCENT Computational Phyloinformatics Workshop

2007-2008 Maria Campo, Commonwealth College Research Fellowship. $1,000

2007-2008 Elsa Petit, Biofuels Research Collaborative. NSM Deans Office. $35,000

2007 Igor Romasko, HHMI Summer Internship. $3,600

2006-2007 Igor Romasko, Commonwealth College Research Fellowship. $1,000

2006-2007 Devin Currie, Life Sciences Junior Fellowship. $1,000

2004-2005 Ana Pereira, Commonwealth College Research Fellowship. $1,000

2004-2005 Wei-Yun Chen, Commonwealth College Research Fellowship. $1,000

2004-2005 Wei-Yun Chen, Life Sciences Junior Fellowship. $1,000

 

INVITED RESEARCH PRESENTATIONS (since 2000)

 

2019 DOE Switchgrass Microbiome Symposium, Berkeley, CA

2018 New England Association of Parasitologists, Northampton, MA

2018 Second Joint Conference on Evolutionary Biology, Montpellier, France

2018 New England BioLabs, Ipswich, MA

2017 Gordon Research Conference on Ecological and Evolutionary Genomics, Biddeford, MA

2016 New England BioLabs, Ipswich, MA

2016 Thünen Symposium on Soil Metagenomics, Braunsweig, Germany

2016 Biology Department, University of Vermont, Burlington, VT

2015 Plant Biology Department, University of Vermont, Burlington, VT

2015 Student Organized NIH Genetics Training Grant Symp., Brandeis University, Waltham, MA

2015 Department of Chemical Engineering, Dartmouth University, Hanover, NH

2014 New England Biology Association of Two-Year Colleges, Enfield, CT

2014 Northeast Naturalist Society, Springfield, MA

2014 Biochemistry Department, University of Missouri, Columbia, MO

2013 American Society for Microbiology, Connecticut River Chapter, Storrs, CT

2013 Ecological Society of America, Minneapolis, MN

2013 Harvard Forest Annual Symposium, Petersham, MA

2013 Plant and Animal Genome XXI, San Diego, CA

2012 Microbiology Graduate Program, University of New Hampshire, Durham, NH

2012 Clostridium XII, Nottingham, UK

2011 Qteros Inc., Marlborough, MA

2011 Amherst College HHMI Genomics Workshop for High School Teachers, Amherst mA

2010 Harvard Forest, Harvard University, Petersham, MA

2010 Clostridium XI, San Diego, CA

2010 STEM Education Institute, Univ of Mass Amherst

2010 Veterinary & Animal Sciences Department, Univ of Mass Amherst

2010 Molecular and Cellular Biology Colloquium, Univ of Mass Amherst

2009 Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT

2009 Amherst College HHMI Genomics Workshop for High School Teachers, Amherst, MA

2008 Sustainable Energy Summit, Amherst, MA

2008 Amherst College HHMI Genomics Workshop for High School Teachers, Amherst, MA

2006 Department of Microbiology, University of Rhode Island, Kingston, RI

2006 Department of Biology, University of Massachusetts at Boston, Boston, MA

2005 Massachusetts Institute of Technology, Boston, MA

2005 UMass Bioinformatics Conference, Lowell, MA

2004 Department of Biology, Boston University, Boston, MA

2004 Graduate Program in Organismal and Evolutionary Biology, UMass Amherst, Amherst, MA

2004 American Academy of Microbiology, Colloquium on System Biology, Portland, OR

2003 Crop Science Society of America/Soil Science Society of America, Denver, CO

2003 Department of Mathematics and Statistics, UMass Amherst, Amherst, MA

2003 Cetek Inc, Marlborough, MA

2003 Molecular Genetics of Bacteria and Phage, Madison, WI

2003 American Society of Pharmacogsny, Chapel Hill, NC

2003 National Institute of Environmental Health Sciences, Raleigh, NC

2003 Department of Neuroscience, University of New Mexico, Albuquerque, NM

2002 FDA Toxicogenomics Workshop, Fayetteville, AK

2002 Institute for Systems Biology, Seattle, WA

2002 Conference on Bioinformatics and Data Integration, Philadelphia, PA

2002 New Mexico Institute of Mining and Technology, Socorro, NM

2002 Linnean Society Symposium, London, UK

2002 University of New Mexico Genomics Symposium, Albuquerque, NM

2002 University of Southern California, Los Angeles, CA

2002 Gordon Research Conference on Molecular Evolution, Ventura, CA

2001 North Carolina State University, Raleigh, NC

2001 Los Alamos National Laboratory, Los Alamos, NM

2001 CHI’s Metabolic Profiling Conference, Boston, MA

2001 Torrey Mesa Research Institute, San Diego, CA

2001 Virtual Bioinformatics and Genomics Conference, Fargo, ND

2001 Santa Fe Institute, Santa Fe, NM

2001 New Mexico Highlands University, Las Vegas, NM

2001 International Conference on Systems Biology, Pasadena, CA

2000 TIGR Computation Genomics Conference, Rockville MD

2000 National University of Singapore, Singapore

2000 Molecular Epidemiology and Evolutionary Genetics of Pathogenic Microorganisms, Hyderabad, India

 

Posters and Presentations by Members of My UMass Research Group

2019 Alex Truchon, Harvard Forest Ecology Symposium, Petersham, MA

2018 Lauren Alteio, LTER Annual Science Meeting, Pacific Grove, CA

2018 Lauren Alteio, International Society for Microbial Ecology, Leipzig, Germany

2018 William Rodriguez, International Society for Microbial Ecology, Leipzig, Germany

2017 Lauren Alteio, DOE JGI Genomics of Energy and Environment Meeting, Walnut Creek, CA

2017 William Rodriguez, Harvard Forest Ecology Symposium, Petersham, MA

2016 Lauren Alteio, Thünen Symposium on Soil Metagenomics, Braunsweig, Germany

2016 William Rodriguez, SACNAS: The National Diversity in STEM Conference, Long Beach, CA

2016 Lauren Alteio, International Society for Microbial Ecology, Montreal, CA

2016 William Rodriguez, International Society for Microbial Ecology, Montreal, CA

2015 William Rodriguez, 7th Annual Soil Metagenomics Conference, Chicago, IL

2015 Lauren Alteio, LTER Annual Science Meeting, Fort Collins, CO

2015 Lauren Alteio, Soil Ecology Society, Colorado Springs, CO

2015 Lauren Alteio, Ecological Society of America Annual Symposium, Baltimore, MD

2015 Kelly Haas, American Society for Microbiology General Symposium, New Orleans, LA

2014 Kelly Haas, Clostridium XIII, San Diego, Shanghai, China

2014 William Rodriguez, 6th Annual Soil Metagenomics Conference, Chicago, IL

2014 Amy Biddle, 5th ASM Conference on Beneficial Microbes, Washington DC

2014 Amy Biddle, Mid-Atlantic Nutrition Conference, Bethesda, MD

2014 William Rodriguez, Harvard Forest Annual Symposium, Petersham, MA

2013 Farah Abdul-Rahman, Society for Molecular Biology and Evolution, Chicago, IL

2013 Kelly Haas, GRC on Applied and Environmental Microbiology, South Hadley, MA

2013 William Rodriguez, Harvard Forest Annual Symposium, Petersham, MA

2012 Amy Biddle, Keystone Symposium on “The Gut Microbiome”, Taos, NM.

2012 Kelly Haas, Clostridium XII, Nottingham, UK

2012 DOE, ARPAE Innovation Summit, Alexandria, VA

2012 Supratim Mukherjee, DOE Grantee and Contractors Workshop, Rockville, MD

2010 Stephen Godin, Clostridium XI, San Diego, CA

2010 Supratim Mukherjee, Clostridium XI, San Diego, CA

2010 Amy Biddle, Argonne Soil Metagenomics Workshop, Chicago, IL

2010 Amy Biddle, International Society for Microbial Ecology, Seattle, WA

2010 Gigi Sun, Society for Molecular Biology and Evolution, Lyon, France

2010 Jinghua Hu, Intelligent Systems for Molecular Biology, Boston, MA

2010 Danielle Amisano, American Society for Microbiology, San Diego, CA

2010 Supratim Mukherjee, American Society for Microbiology, San Diego, CA

2010 Stephen Godin. 2nd Annual TIMBR Conference, Amherst, MA

2010 Amy Biddle, 2nd Annual TIMBR Conference, Amherst, MA

2010 Amy Biddle, DOE Genomes to Life Conference, Rockville, MD

2009 Gigi Sun, International Conference on Genome Biology and Bioinformatics, Atlanta, GA

2009 James Hayes, Gordon Research Conference on Cellulases and Cellulosomes, Andover, NH

2009 Supratim Mukherjee, Gordon Research Conference on Applied & Env. Micro. S. Hadly, MA

2009 Zhiyi Sun, Society for the Study of Evolution, Moscow, ID

2008 Elsa Petit, Clostridium X, Wageningen, NL

2008 Elsa Petit, Boston Bacterial Meeting, Boston, MA

2008 Elsa Petit, American Society for Microbiology, Boston, MA

2008 Zhiyi Sun, Society for the Study of Evolution, Minneapolis, MN

2008 Maria Campo, UMass Undergraduate Research Conference, Amherst, MA

2007 Igor Romashko, Bioconductor Workshop, Seattle, WA

2007 Elsa Petit, Gordon Research Conference on Cellulases and Cellulosomes, Andover, NH

2007 Devin Currie, Gordon Research Conference on Cellulases and Cellulosomes, Andover, NH

2007 Devin Currie, UMass Undergraduate Research Conference, Andover, NH

2007 Jinghua Hu, Gordon Research Conference on Microbial Population Biology, Andover, NH

2006 Jinghua Hu, New England Molecular Evolution Meeting, Amherst, MA

2006 Zhiyi Sun, New England Molecular Evolution Meeting, Amherst, MA

2006 Wei-Yun Chen, American Society for Microbiology, Atlanta, GA

2005 Jinghua Hu, International Conference on Systems Biology, Boston, MA

2005 Ana Pereira, UMass Undergraduate Research Conference, Amherst, MA

2005 Wei-Yun Chen, UMass Undergraduate Research Conference, Amherst, MA

 

PROVISIONAL PATENTS

 

Leschine SB, Blanchard JL, Hagen MJ, Warnick T. Microbial Probiotic culture FLC-2 (C1/C3) and strains PR1, RU2, and SP3 improve fiber digestion to enhance the nutritional value of fibrous animal feed. Filed: Aug 22, 2016

 

PATENTS

 

Blanchard JL, Leschine SB, Petit E, Fabel J, Schmalisch M. Methods and compositions for improving the production of products in microorganisms US Patent 7,943,363 Issued: May 17, 2011

 

TEACHING

 

FELLOWSHIPS

 

2017 UMass Instruction Innovation Fellow

 

AWARDS

 

2007 Thomas G. Lessie Teaching Award in Distinguished Lectureship

 

GRANTS AND CONTRACTS

 

2006-2010 Role: Participant: Elizabeth Conner (PI). Quantitative Systems Biology. HHMI Undergraduate Research Award. $10,000 (total award - $1,600,000)

 

COURSES AND WORKSHOPS TAUGHT

 

University of Massachusetts

2019 Gut Feelings: Learning to foster better microbiome relationships (HONORS391H)

2019 Human Genome Analysis (BIOL597/697GE)

2018 Gut Feelings: Learning to foster better microbiome relationships (HONORS391H)

2018 Evolutionary Genetics (BIOL597/697)

2018 Human Genome Analysis (BIOL597/697GE)

2017 Evolutionary Genetics (BIOL597)

2017 Advanced Genetics (BIOL583)

2017 Microbial Genomics Journal Club (BIOL892)

2016 Evolutionary Genetics (BIOL597)

2016 Advanced Genetics (BIOL583)

2016 Microbial Genomics Journal Club (BIOL892)

2015 Evolutionary Genetics (BIOL597)

2015 Microbial Genomics Journal Club (BIOL892)

2015 Advanced Genetics (BIOL583)

2014 Evolutionary Genetics (BIOL597)

2014 Microbial Genomics Journal Club (BIOL892) - Fall

2014 Microbial Genomics Journal Club (BIOL892) - Spring

2013 Advanced Genetics (BIOL583) – Fall

2013 IPython and the Systems Biology Knowledge Base (Kbase) – 4 day workshop

2013 Microbial Genomics Journal Club (BIOL892)

2013 Advanced Genetics (BIOL583) – Spring

2012 Special Topics in Bioinformatics (BIOL697BI)

2012 Microbial Genomics Journal Club (BIOL892)

2012 Genomics and Bioinformatics (MICBIO660)

2011 Special Topics in Systems Biology (MICBIO697S)

2011 General Microbiology (MICBIO310)

2010 Special Topics in Bioinformatics (MICROBIO697B)

2010 Genomics and Bioinformatics (MICBIO660)

2009 Special Topics in Systems Biology (MICBIO697S): Genome Annotation

2009 General Microbiology (MICBIO310)

2009 Fundamentals of Cellular Engineering (CHEM-ENG 690F)

2008 Special Topics in Systems Biology (MICBIO697S): Advanced Computational Phylogenomics

2008 Bioinformatics Programming (MICBIO590B)

2008 Bioinformatics (CMPSC691K)

2008 Fundamentals of Cellular Engineering (CHEM-ENG 690F)

2007 Special Topics in Systems Biology (MICBIO697S): Microarrays Analysis

2007 Medical Microbiology (MICBIO255)

2007 Genes and Genome Analysis (BIOL397)

2007 General Microbiology (MICBIO310)

2007 Bioinformatics (CMPSC691K)

2006 Special Topics in Systems Biology (MICBIO697S): Metabolic Modeling

2006 Special Topics in Bioinformatics (MICBIO697B)

2006 Bioinformatics Programming (MICBIO590B)

2006 Bioinformatics (CMPSC691K)

2005 Special Topics in Systems Biology (MICBIO697S): Gene Regulatory Modeling

2005 Medical Microbiology (MICBIO255)

2005 General Microbiology (MICBIO310)

2005 Bioinformatics (CMPSC691K)

2004 Bioinformatics (CMPSC691K)

 

BioPharmaceutical Technology Center Institute (One week workshops)

2003 Techniques in Bioinformatics and Comparative Genomics

2003 Computational Approaches to Analyzing Microarray Data

2002 Techniques in Bioinformatics and Comparative Genomics

2002 Computational Approaches to Analyzing Microarray Data

2001 Techniques in Bioinformatics and Comparative Genomics

2000 Techniques in Bioinformatics and Comparative Genomics

2000 Database Structure and Design for Genomics Research

1999 Techniques in Bioinformatics and Comparative Genomics

 

National Center for Genome Resources

2002 NCGR’s Winter Bioinformatics Workshop

2002 Mentor for NSF Minority Training Program

2001 Mentor for NSF Minority Training Program

 

STUDENTS AND POSTDOCS MENTORED IN MY LABORATORY

 

University of Massachusetts

 

  1. Arianna Kazemi, Biochemistry, In Progress

  2. Hanna Choi, Biology, In Progress

  3. Eliza Holtz, Biology, In Progres

  4. Young Il Choi, In Progress

  5. Eva Trip, Biology, In Progress

  6. Andrea Dame, Microbiology, In Progress

  7. Lionel Forbes, Biology, In Progress

  8. Nathan Haywood, B.S., Biochemistry, In Progess

  9. Karen Luong, REU, LEE-SIP 2018, In Progress

  10. Heidi Mannarino, Environmental Sciences, 2019

  11. Nadia L’Bahy, B.S., Biology, 2018

  12. Matthew Kuhl, REU, Collaborative Undergraduate Research in Energy Program 2018

  13. Victoria Thong, B.S., Biology, 2017-2018

  14. Aria Jordan, B.S., Biochemistry, 2017-2019

  15. Jacob Barnet, Ph.D., Organismal and Evolutionary Biology, 2017-2018

  16. Alexander Truchon, B.S., Microbiology, In Progress

  17. Nick Mucci, B.S., Biology, 2017

  18. Aaron Szczepanek, B.S., Biology, 2017

  19. Rebeca Bonilla, REU, Harvard Forest Summer Internships Ecological Research 2016

  20. Belle Henry, REU, Collaborative Undergraduate Research in Energy Program 2016

  21. Jonathan Hulvey, Ph.D., Research Assistant Professor, 2014-2017

  22. Lauren Alteio, Ph.D., Organismal and Evolutionary Biology, In Progress

  23. William Rodriguez, Ph.D., Organismal and Evolutionary Biology, In Progress

  24. Nadia Kianfar, B.S., Biology, In Progress

  25. Kelly Haas, Ph.D., Microbiology 2016

  26. Kelly Callahan, B.S., Veterinary and Animal Sciences 2016

  27. Shane Lawson, B.S. BMB 2016

  28. Madhura Kulkarni, B.S. BMB 2016

  29. Fauzia Iqbal, B.S. Microbiology 2016

  30. Ava Bakhtyari, B.S. BMB 2016

  31. Josia DeChiara, REU, Harvard Forest Summer Internships Ecological Research 2015

  32. Cora Kerber, REU, Collaborative Undergraduate Research in Energy Program 2015

  33. Eric Gann, B.S., Biology, B.S. BMB 2015

  34. Jacob Mayfield, Ph.D., Research Fellow 2014 – 2015

  35. Josia DeChiara, B.S., Biology (Hampshire College), 2014-2015

  36. Ada Vilches, REU, Harvard Forest Summer Internships Ecological Research 2014

  37. Nuria Varela, REU, Collaborative Undergraduate Research in Energy Program 2014

  38. Sonia Filipczak, B.S., Public Health 2014

  39. Monique Tait, M.S., Microbiology 2014

  40. Maddy Coppi, Ph.D. Research Assistant Professor, 2010-2013

  41. Sonia Filipczak, REU, Harvard Forest Summer Internships Ecological Research 2014

  42. Farah Abdul-Rahman, M.S., Microbiology 2013

  43. Josephine Aiyeku, B.S. Microbiology 2013

  44. Megan Strough, M.S. Microbiology 2013

  45. Amy Biddle, Ph.D., Microbiology 2013

  46. James Hayes, M.S., Molecular and Cellular Biology, 2013

  47. Supratim Mukherjee, Ph.D., Microbiology, 2013

  48. Tara Mahendrarajah, B.S., Microbiology 2012

  49. Farah Abdul-Rahman, B.S., Microbiology 2012

  50. Ana Jenness, B.S., Microbiology 2012

  51. Deepti Sreepathi, B.S., Microbiology 2012

  52. Tara Mahendrarajah, REU, Harvard Forest Summer Internships Ecological Research 2011

  53. Kelden Pehr, REU, Harvard Forest Summer Internships Ecological Research 2011

  54. Caitlin Lauer, B.S., Microbiology 2011

  55. Stephen Godin, B.S., Biology 2011

  56. Zhiyi Sun, Ph.D., Organismal and Evolutionary Biology 2011

  57. Michael Abdelshahid, REU, Institute for Cellular Engineering 2010

  58. Maria Campo, M.S., Molecular and Cellular Biology 2010

  59. Atamurad Chariyeva, B.S., Computer Science 2010

  60. Danielle Amisano, B.S., Microbiology 2009, M.S. Microbiology 2010

  61. Elsa Petit, Ph.D., Postdoctoral Fellow 2010

  62. Volker Grabe, M.S. Bioinformatics (visiting student from Germany)

  63. Jinghua Hu, Ph.D., Electrical and Computer Engineering 2008

  64. Igor Romashko, B.S., Biochemistry 2008, B.S., Computer Science 2008

  65. Supriya Deshpande, Intern 2007-2008

  66. Devin Currie, B.S., Microbiology 2007

  67. Benjamin Sanders, Microbiology (left after one year for medical school) 2007

  68. Angelle Aldridge, B.S., University Without Walls Off Campus 2007

  69. Ana Pereira, B.S., Microbiology 2005, M.S., Microbiology 2008

  70. Winnie Chen, B.S., Microbiology 2005, M.S., Microbiology 2006

  71. Andrew Tolopko, B.S., Computer Science 2005

 

National Center for Genome Resources

72. Robert Küffner, Ph.D., Current position: Senior Bioinformaticist, Ludwig Maximilians Unversität München

 

SERVICE

 

SERVICE TO DISCIPLINE

 

Grant Review

Ad hoc reviewer. USDA NIFA. 2019

Ad hoc reviewer. US-Israel Binational Science Foundation. 2019

Panel Member. DOE. 2018

Panel Member. NSF. 2018

Panel Member. DOE 2018

Panel Member. NSF. 2018

Panel Member. DOE 2017

Panel Member. DOE 2016

Panel Member. DOE 2016

Ad hoc reviewer. USDA NIFA. 2016

Ad hoc reviewer. NSF 2015

Panel Member. DOE 2015

Panel Member. NSF. 2015

Panel Member. DOE 2014

Ad hoc reviewer. NSF 2014

Panel Member. NSF 2014

Panel Member. DOE 2014

Panel Member. DOE  2014

Ad hoc reviewer. Agentscahp voor Innovatie door Wetenschap en Technologie (Belgium). 2013

Panel Member. NSF 2012

Panel Member. NSF 2011

Panel Member. NSF  2011

Ad hoc reviewer. Human Frontier Science Program (Germany HQ). 2011

Panel Member. DOE 2011

Panel Member. NSF  2010

Panel Member. USDA-CREES Climate Research. 2009-2010

Panel Member. DOE  2009

Panel Member. NSF 2009

Ad hoc reviewer. NSF 2009

Ad hoc reviewer. Smithsonian Institution International Program. 2008

Ad hoc reviewer. NSF Division of Mathematical Sciences. 2008

Panel Member. Center for Apoptosis Research. 2007

DOE site review for Shewanella Project. 2006

Ad hoc reviewer. Michael Smith Health Research Foundation, Canada. 2005
Ad hoc reviewer. NSF/USDA/DOE Microbial Genome Program. 2005

Panel Member. DOE Microbial Genome Program. 2004

Ad hoc reviewer. NSF Division of Mathematical Sciences. 2004

Site review panel - National Institute of Environmental Health Sciences. 2003

 

Editorial Boards

Editorial Board for BMC Genomics 2015 -

Editorial Board for PLOS ONE 2013 -

Editorial Board for Journal of Biochemical and Microbial Technology. 2012 -

 

Journals Refereed

Applied and Environmental Microbiology

Biochemistry

Biofuels for Biotechnology

Canadian Journal of Microbiology

Environmental Microbiology

Evolution

FEMS Microbial Ecology

Frontiers in Plant Sciences

Gene

Genetica

Genome Research

Genome Biology and Evolution

Journal of Molecular Evolution

Journal of Phycology

Life

Molecular Biology and Evolution

Microbial Pathogenesis

Metabolic Engineering

Nature

Nature Microbiology

PLoS One

Proceedings of the Royal Society B

Science

Trends in Microbiology

 

Other

 

Lead Organizer for a workshop on a NSF workshop “Advanced Analysis of Genomic Data in Microbial Ecology Research” for the National Ecological Observatory Network. Boulder, CO. 2014

Co-Organizer of mini-symposium on “Manipulating the Gut Microbiome for Human Health” for the Center for Clincal and Translational Science. Worcester, MA. 2014

Graduate Program Review, University of New Hampshire. 2014

Institutional representative to the National Ecological Observatory Network. 2011-

International Program Committee, Foundations of Systems Biology in Engineering. 2009

Microbial Population Biology Gordon Conference Session Chair. 2005

 

SERVICE TO UNIVERSITY

 

Grant Review

Mahoney Life Sciences Prize Review Committee. 2018, 2019

Ad hoc reviewer for Faculty Research Grants. 2018

Mahoney Life Sciences Prize Review Committee. 2017

OEB Research Grant Committee. 2017

Ad hoc reviewer for Faculty Research Grants. 2011

Ad hoc reviewer. Center for Apoptosis Research. 2010

Ad hoc reviewer for Faculty Research Grants. 2006

Ad hoc reviewer for Faculty Research Grants. 2005

Ad hoc reviewer for Lotta Crabtree Fellowships. 2005

Commonwealth College Research Grants and Fellowships. 2004

 

Committee Assignments

 

Graduate Committee Advisor (23 PhD students, 7 Masters students)

Chair, Microbiology Faculty Search Committee. 2018

OEB Seminar Committee. 2016-

Institutional Biosafety Committee 2014 -

Biology Internet Technologies Committee. 2013-2016

MCB Graduate Advising Committee. 2011-2015

Biology Research Committee. 2012-2013

MCB Seminar Organizer. 2011-2013

Biology Faculty Search Committee. 2013

Chair, Microbiology Faculty Search Committee. 2010

Plant, Insect & Soil Science Search Committee. 2010

Deans Graduate Curriculum Group. 2009-2010

Veterinary & Animal Science Search Committee. 2008

OEB AQAD review participant. 2008

OEB Graduate Program Admissions Committee. 2006-2010

OEB Steering Committee. 2004-

Microbiology Graduate Program Admissions Committee. 2003-2010

Biochemistry Faculty Search Committee. 2006

Microbiology Genomics Search Committee. 2005

Vice Chancellor Search Committee. 2004

 

Other

 

Member, Institute for Bioinformatics, Biostatistics and Computational Biology, UMass Amherst 2011-

Member, Center for Clinical and Translational Science, UMass Med, Worcester 2010-Member, The Institute for Cellular Engineering, UMass, Amherst 2008-Member, The Massachusetts Institute for Biofuels Research (TIMBR), UMass, Amherst 2007-

Worked with consultant on improving visibility of UMass Life Sciences research. 2012

Life Science Strategic Planning Industry workshop. 2012

Life Science Strategic Planning PVLSI workshop. 2012

Interviewed job candidate for CVIP. 2011

Recruited students at the University of Puerto Rico Mayaqüez. 2009, 2010

Freshman Orientation Presentation. 2011

Life Sciences Laboratory Core Facilities Design Team. 2009-2010

CNS Committee on Interdisciplinary Graduate Education. 2010

Reviewed abstracts for UMass undergraduate research symposium. 2003-

Biosciences Talent Advancement Program Speaker. 2006

Microbiology representative for open houses for prospective undergraduate students. 2006, 2007

Microbiology representative for Science Research Opportunities Fair. 2008

 

OUTREACH

 

Industry Advisory Boards

 

Technical Advisory Board, Qteros. 2007- 2008

Technical Advisory Board, Physiome Sciences. 2003

 

Other Service

 

Science Cafe. Gut Feeling: Fostering a diverse and healthy microbiome. 2015

Tours of LSL for prospective community college transfer students. 2014

UMass STEM K-12 Teachers Workshop. Backyard Biofuels. 2011

Amherst College HHMI Genomics Workshop for High School Teachers. 2008, 2009, 2011

Faculty Advisor, Society of Undergraduate Microbiology Majors. 2005

Presentation for National DNA Day at Westfield High School. 2005

Presentations for Biotechnology Day at Gateway High School. 2004