The Hazen Lab

Plant Regulatory Genomics

@ University of Massachusetts Amherst

TRANSCRIPTION REGULATORY CIRCUITS OF PLANT BIOMASS ACCUMULATION

NATURAL GENETIC DIVERSITY AND GENOMIC RESOURCES

PLANT-MICROBE RHIZOSPHERE INTERACTIONS

 
 

2010 - present

MacKinnon KJM, ColeBJ, Yu C, Coomey JH, Hartwick, Remigereau MS, Duffy T, Michael TP, Kay SA, Hazen SP (in review) Thermocycles are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. https://doi.org/10.1101/762021

Zhao K, Lin F, Romero-Gamboa SP, Saha P, Goh H-J,  An G, Jung K-H, Hazen SP, Bartley LE (2019) Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis. Frontiers in Plant Sciencedoi: 10.3389/fpls.2019.01275.

McCahill IW, Hazen SP (2019) Regulation of cell wall thickening by a medley of mechanisms. Trends in Plant Science24:853-866.

Jansson C, Mockler T, Vogel JP, De Paoli H, Hazen SP, Srinivisan V, Cousins A, Lemaux P, Dahlberg J, Brutnell T (2019) A perspective on a paradigm shift in plant photosynthesis: designing a novel type of photosynthesis in sorghum by combining C3 and C4 metabolism. In Oxygen Production and Reduction in Artificial and Natural Systems. (Eds Barber J, Ruban AV, Nixon PJ). Chapter 19, pp 397-411. World Scientific Publishing Co. Pte, Ltd, New Jersey, U.S.A.

Olins JR*, Lin L*, Lee SJ, Trabucco GM, MacKinnon KJ-M, Hazen SP (2018) Secondary wall regulating NACs differentially bind at the promoter at a CELLULOSE SYNTHASE A4 cis-eQTL. Frontiers in Plant Science. 9:1895.

Handakumbura PP, Brow K, Whitney IP, Zhao K, Sanguinet KA, Lee SJ, Olins J, Romero-Gamboa SP, Harrington MJ, Bascom CJ, MacKinnon KJ-M, Veling MT, Liu L, Lee JE, Vogel JP, O’Malley RC, Bezanilla M, Bartley LE, Hazen SP (2018) SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae. The Plant Journal96:532-545.

Jansson C, Vogel JP, Hazen SP, Brutnell TP, Mockler TC (2018) Climate-smart crops with enhanced photosynthesis. Journal of Experimental Botany 69: 3801-3809.

Dixit A, Toma P, Vaine E, Hexham A, Hazen SP, Dhankher OP (2018) A stress-associated protein, AtSAP13, from Arabidopsis thaliana provides tolerance to multiple abiotic stresses. Plant, Cell & Environment 41:1171-1185.

da Costa RMF, Pattathil S, Avci U, Lee SJ, Hazen SP, Winters A, Hahn MG, Bosch M (2016) A cell wall reference profile for Miscanthus bioenergy crops highlights compositional and structural variations associated with development and organ origin. New Phytologist 213:1710-1725.

Tyler L, Lee SJ, Young N, Delulio GA, Benavente E, Reagon M, Sysopha J, Baldini RM, Troia A, Hazen SP, Caicedo AL (2016) Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. The Plant Genome 9(2).

Alvelo-Maurosa JG, Lee SJ, Hazen SP, Leschine SB (2016) Direct image-based enumeration of Clostridium phytofermentans cells on insoluble plant biomass growth substrates. Applied and Environmental Microbiology 82: 972-978.

Coomey J, Hazen SP (2016) Brachypodium distachyon as a model species to understand grass cell walls. In Genetics and Genomics of Brachypodium (ed. JP Vogel), Springer, NY. pp 197-217.

López-Alvarez D, Manzaneda AJ, Rey PJ, Giraldo P, Benavente E, Allainguillaume J, Mur L, Caicedo AL, Hazen SP, Breiman A, Ezrati S, Catalán P (2015) Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range. American Journal of Botany 102:1-16.

Taylor-Teeples M*, Lin L*, de Lucas M*, Turco G, Toal TW, Gaudinier A,Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Corwin J, Tsoukalas N, Pauly M, Kliebenstein DJ, Tagkopoulos I, Breton G, Pruneda-Paz JL, Ahnert SE, Kay SA, Hazen SP†, Brady SM† (2015) An Arabidopsis gene regulatory network for xylem specification and secondary wall biosynthesis. Nature 517: 571-575.

Li L, Zhang Q, Pedmale UV, Nito K, Fu W, Lin L, Hazen SP, Chory J (2014) PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Molecular Plant 7: 1582-1585.

Matos DA, Cole B, Whitney IP, MacKinnon KJ-M, Kay SA, Hazen SP (2014) Daily changes in temperature, not the circadian clock, regulate growth rate in Brachypodium distachyonPLoS ONE 9: e100072.

da Costa R, Lee SJ, Allison GA, Hazen SP, Winters A, Bosch M (2014) Characterization of the biomass properties of 25 genotypes of the lignocellulosic energy crop MiscanthusAnnals of Botany 114: 1265-1277.

Matos DA, Whitney IP, Harrington MJ, Hazen SP (2013) Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode. PLoS ONE8:e80640.

Handakambura PP, Matos DA, Osmont KS, Harrington MJ, Heo K, Kafle K, Kim SH, Baskin TI, Hazen SP (2013) Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls. BMC Plant Biology13: 131.

Trabucco GM, Matos DA, Lee SJ, Saathoff AJ, Priest HD, Mockler TC, Sarath G, Hazen SP (2013) Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyonBMC Biotechnology13:61.

Handakumbura P, Hazen SP (2012) Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Frontiers in Plant Science3:74.

Lee SJ, Warnick TA, Pattathil S, Alvelo-Maurosa JG, Serapiglia MJ, McCormick H, Brown V, Young NF, Schnell DJ, Smart LB, Hahn MG, Pedersen JF, Leschine SB, Hazen SP (2012) Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality. Biotechnology for Biofuels5:5.

Lee SJ, Warnick TA, Leschine SB, Hazen SP (2012) A high-throughput biological conversion assay for determining lignocellulosic quality. Methods in Molecular Biology918:341-349.

Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt III BF, Hong S-Y, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LAJ, Park C-M, Sedbrook J, Watt M, Zheng SJ, Vogel JP (2011) Brachypodium as a model for the grasses: Today and the future. Plant Physiology153:3-13.

The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyonNature463:763-768.

2005-2009

Hazen SP, Naef F, Quisel T, Borevitz JO, Gendron JM, Kay SA (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biology10:R17.

Michael TP, Breton G, Hazen SP, Priest HD, Mockler TC, Kay SA, Chory JA (2008) Morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biology6:e225.

Garvin DF, Gu Y, Hasterok R, Hazen SP, Jenkins G, Mockler TP, Mur L, Vogel JP (2008) Development of genetic and genomic resources for Brachypodium distachyon, a new model system for grass crop research. The Plant Genome48:S-69-S-84.

Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Priest HD, Sullivan CM, Shen R, Givan SA, Yanovsky M, Hong F, Kay SA, Chory JA (2008) Network discovery pipeline elucidates conserved time of day specific cis-regulatory modules. PLoS Genetics4:e14.

Borevitz JO, Hazen SP, Michael TP, Morris GP, Baxter I, Hu TT, Chen H, Werner J, Salt D, Kay SA, Chory J, Weigel D, Nordborg M, Jones JDG, Ecker JR (2007) Genome wide patterns of single feature polymorphism diversity in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA29:12057-12062.

Rensink WA, Hazen SP (2006) Statistical issues in microarray data analysis. In J Salinas, JJ Sanchez-Serrano (eds.), Methods in Molecular Biology, vol. 323: Arabidopsis Protocols, Second Edition Humana Press Inc., Totowa, NJ. pp 359-366

Singer TS, Fan Y, Chang H-S, Zhu T, Hazen SP, Briggs SP (2006) A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome array hybridization. PLoS Genetics. 2:e144.

Hazen SP, Pathan MS, Sanchez AC, Baxter I, Dunn M, Estes B, Chang H-S, Zhu T, Kreps JA, Nguyen HT (2005) Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Functional and Integrative Genomics5:104-116.

Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005) LUX ARRHYTHMO encodes a Myb transcription factor essential for circadian rhythms. Proceedings of the National Academy of Sciences, USA. 120:10387-10392.

Hazen SP, Borevitz JO, Harmon FG, Pruneda-Paz JL, Schultz TF, Yanovsky MJ, Liljegren SJ, Ecker JR, Kay SA (2005) Rapid array mapping of circadian clock and developmental mutations in ArabidopsisPlant Physiology138:990-997.

Baxter IR, Young JC, Armstrong G, Foster N, Bogenschutz N, Cordova T, Peer WA, Hazen SP, Murphy AS, Harper JF (2005) A plasma membrane H+-ATPase is required for the formation of proanthocyanidins in the seed coat endothelium of Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA102:2649-2654.

prior to 2005

Hazen SP, Kay SA (2003) Gene arrays aren’t just for measuring gene expression. Trends in Plant Science 8:413-416.

Hazen SP, Wu Y, Kreps JA (2003) Gene expression profiling of plant response to abiotic stress. Functional and Integrative Genomics 3:105-111. 

Hazen SP, Hawley RM, Davis GL, Henrissat B, Walton JD (2003) Quantitative trait loci and comparative genomics of cereal cell wall composition. Plant Physiology 132:263-271.

Hazen SP, Scott-Craig JS, Walton JD (2002) Cellulose synthase-like (CSL) genes of rice. Plant Physiology 128:336-340.

Hazen SP, Leroy P, Ward RW (2002) AFLP in Triticum aestivum L.: patterns of genetic diversity and genome distribution. Euphytica125:89-102.

Hazen SP, Zhu L, Kim HS, Tang G, Ward RW (2002) Genetic similarity of winter wheat in Shaanxi province, China and other common wheat germplasm pools. Genetic Resources and Crop Evolution49:439-448.

Hazen SP, Ng PKW, Ward RW (1997) Variation in grain functional quality for soft winter wheat. Crop Science. 37:1086-1093.

Hazen SP, Ward RW (1997) Variation in soft winter wheat characteristics measured by the single kernel characterization system. Crop Science37:1079-1086.

PEOPLE

 

SAM HAZEN

Principal Investigator

JOSH COOMEY

Plant Biology Graduate Student

KIRK MACKINNON

Molecular and Cellular Biology Graduate Student

IAN MCCAHILL

Plant Biology Graduate Student

GREG GREGORY

Rotating Plant Biology Graduate Student

ALDEN NICHOLS

Undergraduate Lab Assistant

EMMA O'DONNELL

Undergraduate Lab Assistant

RITHANY KHEAM

Undergraduate Lab Assistant

KIRA GARDNER

Undergraduate Lab Assistant

JOJO COLEMAN

Undergraduate Lab Assistant

CYNTHIA GUZMAN

Undergraduate Lab Assistant

NICOLE LEBLANC

Undergraduate Lab Assistant

LAB ALUMNI

Postdoctoral Fellows

Naomi Young, Technical Project Manager, Koppers Performance Chemicals, Worcester, UK

Li Lin, Plant Reproductive Biologist, Bayer Crop Science, St. Louis, MO

Michael Harrington, Chief Executive Officer, Genoverde Bioscience Inc., Raleigh, NC

Anirudha Dixit, Senior R&D Scientist, NASA, Kennedy Space Station, FL

PhD Graduate Students

Pubudu Handakumbura, Staff Scientist, Pacific Northwest National Laboratory, Richland WA

Scott Lee, Postdoc, Donald Danforth Plant Science Center, St. Louis MO

Sandra Romero-Gamboa, Staff Scientist, Verinomics Inc., New Haven CT

MS Graduate Students

Dominick Matos, Graduate Student, Harvard University, Programs in Biomedical and Biological Sciences

Gina Trabucco, Scientific Associate II, Novartis Institutes for Biomedical Research, Cambridge MA

Ian Whitney, Sequencing Solutions Specialist, Roche, St. Louis, MO

Dennis DePaolo, Cultivation Advisor/Manager at Standard Wellness Company, LLC

Postbaccalaureate Research Fellows

Miriam Hernandez-Romero, Graduate Student, University of Massachusetts, Plant Biology

Undergraduate Researchers

Peter MacAskill, Lab Technician,
Bringham & Woman's Hospital/Harvard Medical School, Boston MA

Torie Caroll, Business Development Associate, Acorio, Boston, MA

Rebecca Lamothe, Graduate student, University of California Berkeley, Molecular and Cellular Biology Program

Scott Barish, Graduate Student,
 Duke University, Cellular and Molecular Biology Program

Michael Veling, PhD, Postdoc, Harvard University 

Jessica Sysopha, Laboratory Technician, IEH Laboratories & Consulting Group, Providence, RI

Nicholas Fitzgerald, Process Development Associate, Broad Institute of MIT and Harvard, Cambridge, MA

Annie Mombourquette, MPH, Substance Use Prevention Coordinator, San Juan Basin Public Health, Durango, CO

Kathryn Brow, Student, Birthwise Midwifery School

Rachel Dannay, Laboratory Technician, Washington State University, Pullman, WA

Chrismery Gonzalez, MPH, Field Supervisor for the City of Springfield-Dept. of Human and Health Service and Program Coordinator for MotherWoman, Springfield, MA

Julia Deane, Clinical Trial Monitor at Dana-Farber Cancer Institute, Boston, MA

Paul O’Connor, Graduate Student, University of Massachusetts

Jenny Olins, MS, Research Associate, Beam Therapeutics, Cambridge, MA

Evan Rees, Graduate Student, Cornell University, Plant Breeding and Genetics

Julie Webb, Graduate Student, University of Connecticut, Geoscience Program

Natasha Ando, Senior Process Executive, Cognizant, Ontario, Canada

Jess Mazzola, Cell Culture Production Associate, Organogenesis Inc., Canton, MA

Grace Stroman, Scientist, Merck, Cambridge, MA 

Chang Yu, Graduate Student, Brown University, Biostatistics Program

Kathryn Santos

Yefeng Ethan Wang

Rebecca Yeh, Research Assistant, Boston Children's Hospital

Katie Krasnoff, Research Associate, HelixBind, Marlborough, MA

Summer Research Interns

Samantha Waterhouse, TM Chemist, Abbott, Scarborough, ME

Ryan Spector, QA Chemist at Estee Lauder

Baxter Worthing, Graduate Student, University of Vermont

Fahmida Saki, Undergraduate student at National Technical Institute for the Deaf

Emily Sidansky, Undergraduate student at Rochester Institute of Technology

Signe Tarmey, Nursing Student, University of Texas Tyler

Idania Perez, Undergraduate student at National Technical Institute for the Deaf

Lindsey Gnage, Undergraduate student at National Technical Institute for the Deaf

 

DIVERSITY

The Hazen Lab is a safe space, where we value diversity, and firmly believe that it is a critical component of excellence. 

 

EVENTS

 
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GRADUATE TRAINING

I train graduate students in the Plant Biology and the Molecular and Cellular Biology Graduate Programs. Students are accepted into a program rather than directly into a laboratory. All students admitted into these programs rotate in three labs during their first year. After this experience, students settle into a laboratory where there is sufficient interest and adequate resources.

 

ADDRESS

WHERE TO FIND US
N427 Life Science Laboratories
240 Thatcher Way
Amherst, MA

ADDRESS

MAILING ADDRESS
Biology Department
221 Morrill Science Center III
University of Massachusetts
Amherst, MA 01003

CONTACT

hazen@bio..umass.edu
LAB 413-545-6045
OFFICE 413-545-4546

 
 

©2018 by University of Massachusetss Amherst

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