The Hazen Lab
Plant Regulatory Genomics
@ University of Massachusetts Amherst
REGULATION OF CELL WALL GROWTH
NATURAL GENETIC DIVERSITY AND GENOMIC RESOURCES
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PLANT-MICROBE RHIZOSPHERE INTERACTIONS
DIVERSITY
The Hazen Lab is a safe space, where we value diversity, and firmly believe that it is a critical component of excellence.
PUBLICATIONS
2020 - present
McCahill IW, Khahani B, Probert CF, Flockhart EL, Abushal LT, Gregory GA, Zhang Y, Baumgart LA, O'Malley RC, Hazen SP (2024) Shoring up the base: the development and regulation of cortical sclerenchyma in grass nodal roots. bioRXiv. doi.org/10.1101/2024.01.25.577257. Web tool to explore root RNA-seq gene expression data.
Coomey JH, MacKinnon KJ-M, McCahill IW, Khahani B, Handakumbura PP, Trabucco GM, Mazzola J, Leblanc NA, Kheam R, Hernandez-Romero M, Barry K, Liu L, Lee JE, Vogel JP, O’Malley RC, Chambers JJ, Hazen SP (in press) Mechanically induced localization of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression. Quantitative Plant Biology also bioRXiv. Web tool to explore mechanical stimulus time course gene expression data.
Hasterok R, Catalan P, Hazen SP, Roulin A, Vogel J, Wang K, Mur L (2022) Brachypodium: Twenty years as a grass model, the way forward? Trends in Plant Sciences. 27:1002-1016.
Coomey JH, Sibout R†, Hazen SP† (2020) Grass cell walls, Brachypodium distachyon as a model for discovery. New Phytologist. 227:1709-1724.
MacKinnon KJ-M, Cole BJ, Yu C, Coomey JH, Hartwick NT, Remigereau M-S, Duffy T, Michael TP, Kay SA, Hazen SP (2020) Thermocycles are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation. New Phytologist. 227:1649-1667.
Web tool to explore time course gene expression data.
Gordon SP, Contreras-Moreira B, Levy JJ, Djamei A, Czedik-Eysenberg A, Markham V, Session A, Martin J, Cartwright A, Katz A, Singn V, Goltsman E, Barry K, Dinh-Thi VH, Chalhoub B, Diaz-Perez A, Sancho R, Lusinska J, Wolny E, Nibau C, Doonan JH, Mur L, Plott C, Jenkins J, Hazen SP, Lee SJ, Shu S, Goodstein D, Rokhsar D, Schmutz J, Hasterok R, Catalan P, Vogel JP (2020) Gradual polyploid genome evolution revealed by a pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications. 11, 3670.
2015 - 2019
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 Science. 10:1275.
McCahill IW, Hazen SP (2019) Regulation of cell wall thickening by a medley of mechanisms. Trends in Plant Science. 24:853-866.
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 Journal. 96:532-545.
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, Abdullah H, 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).
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.
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.
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.
2010-2014
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 distachyon. PLoS 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 Miscanthus. Annals 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 ONE. 8: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 Biology. 13: 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 distachyon. BMC Biotechnology. 13:61.
Handakumbura P, Hazen SP (2012) Transcriptional regulation of grass secondary cell wall biosynthesis: playing catch-up with Arabidopsis thaliana. Frontiers in Plant Science. 3:74.
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 Biofuels. 5:5.
Lee SJ, Warnick TA, Leschine SB, Hazen SP (2012) A high-throughput biological conversion assay for determining lignocellulosic quality. Methods in Molecular Biology, 918:341-349.
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 Physiology. 153:3-13.
The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.
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 Biology. 10: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 Biology. 6: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 Genome. 48: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 Genetics. 4: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, USA. 29:12057-12062.
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 Genomics. 5:104-116.
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 Arabidopsis. Plant Physiology. 138:990-997.
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, USA. 102:2649-2654.
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. Euphytica 125:89-102.
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 Evolution. 49:439-448.
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 Science. 37:1079-1086.
PEOPLE
A Collaborative & Diverse Group
SAM HAZEN
Principal Investigator
GREG GREGORY
Plant Biology Graduate Student
BAHMAN KHAHANI
Plant Biology Graduate Student
SHELBY BOULANGER
Plant Biology Graduate Student
LOGAYN ABUSHAL
Plant Biology Graduate Student
THI TRAN
Undergraduate Lab Assistant
LILY GIGANTE
Undergraduate Lab Assistant
EDWARD LI
Undergraduate Lab Assistant
VALERIA LACOUTURE
Undergraduate Lab Assistant
SERENE OMRAN
Undergraduate Lab Assistant
SOPHIA RINALDI
Undergraduate Lab Assistant
KYLIE CAMPANA
Undergraduate Lab Assistant
KATIE MCGILLIVRAY
Undergraduate Lab Assistant
KALIEGH WEEKS
Undergraduate Lab Assistant
ERICA WEINSTEIN
Undergraduate Lab Assistant
LAB ALUMNI
Postdoctoral Fellows
Naomi Young,Senior Manager Category Safety Aircare & PestSenior Manager Category Safety Aircare & Pest. Reckitt, Oxfordshire, 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 Scientist, Amentum, Kennedy Space Station, FL
PhD Graduate Students
Pubudu Handakumbura, Team Lead, Pacific Northwest National Laboratory, Richland WA
Scott Lee, Bioinformatics Lead, Yield10 Biosciences, Woburn MA
Sandra Romero-Gamboa, Staff Scientist, Verinomics Inc., New Haven CT
Joshua Coomey, Postdoc, Washington University, St. Louis MO
Kirk MacKinnon, Postdoc, New York University, New York NY
Ian McCahill, Postdoc, MIT, Cambridge, MA
MS Graduate Students
Dominick Matos, PhD, Scientist at Simcere Innovation, Cambridge MA
Gina Trabucco, Senior Scientist 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
Victoria Saleem, SVP of Sales, GlideFast Consulting, San Jose, CA
Rebecca Lamothe, PhD, Scientist at Metagenomi, Emeryville CA
Scott Barish, PhD, Postdoc, Baylor College of Medicine, Houston TX
Michael Veling, PhD, Senior Scientist, Discovery Biology, Acton, MA
Jessica Sysopha, Laboratory Technician, IEH Laboratories & Consulting Group, Providence, RI
Nicholas Fitzgerald, Laboratory Coordinator, Broad Institute of MIT and Harvard, Cambridge, MA
Crysta Daniels, Plant Health Care Technician, Hartney Greymont, Needham, MA
Annie Mombourquette, MPH, Systems Change Specialist, Colorado Department of Public Health and Environment, Denver, CO
Kathryn Brow, Student, Birthwise Midwifery School
Rachel Dannay, Senior Research Assistant, Vaccine and Gene Therapy Institute, Portland, OR
Chrismery Gonzalez, MPH, Lead, Office of Racial Justice and Health Equity, Springfield, MA
Julia Deane, Clinical Trial Manager, TransMedics, Inc, Wakefield, MA
Paul O’Connor, Graduate Student, University of Massachusetts
Jenny Olins, MS, Associate Director, Analytical Development Lead, Beam Therapeutics, Cambridge, MA
Evan Rees, MS, Software Engineer, Embark Veterinary, Ithaca, NY
Julie Webb, MS, GIS Application Developer, Boston Planning & Development Agency, Boston, MA
Natasha Ando, Business Analyst I, TELUS, Ontario, Canada
Jess Mazzola, Cell Culture Production Associate, Organogenesis Inc., Canton, MA
Grace Stroman, Graduate Student, University of North Carolina, Chapel Hill, NC
Madelaine Boyle, Build Engineer 3, Gingko Bioworks, Cambridge, MA
Chang Yu, Graduate Student, Brown University
Kathryn Santos, Clinical Research Assistant, Dana-Farber Cancer Institute
Yefeng Ethan Wang, Senior Research Associate, Sanofi, Cambridge, MA
Rebecca Yeh, Genetics Counseling Program, MGH Institute of Health Professions, Boston, MA
Katie Krasnoff, Senior Research Associate, Sherlock Biosciences, Watertown, MA
Alden Nichols, Clinical Trials Associate, ICON pic, Dublin, Ireland
Nicole Leblanc, Rapid Genomics, Gainesville, FL
Emma O'Donnell, Associate Scientist, Blueprint Medicine, Cambridge, MA
Kira Gardner, Graduate Student, Duke University, Durham, NC
Harshini Parakh, Graduate Student, Brown University, Providence
Emil Mah, Graduate Student, Boston University, Boston, MA
Cassandra Probert, Graduate Student, Vanderbilt University, Nashville, TN
Eleah Flockhart, Graduate Student, Colorado State University, Fort Collins, CO
Summer Research Interns
Samantha Waterhouse, TM Chemist, Abbott, Scarborough, ME
Ryan Spector, QA Chemist at Estee Lauder
Baxter Worthing, PhD, Oak Ridge National Laboratory, Oak Ridge, TN
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, Specimen Management Technician, ACM Medical Laboratory, Spencerport, NY
Abraham Polenco, Undergraduate student at Gallaudet University
Ellie Warren, Undergraduate student at National Technical Institute for the Deaf/Rochester Institute of Technology
Desmond Almanza, Undergraduate student at National Technical Institute for the Deaf/Rochester Institute of Technology
Aubrey Santoro, Undergraduate student at Rochester Institute of Technology
GRADUATE TRAINING
I train graduate students in the Plant Biology Graduate Program. Students are accepted into the program rather than directly into a laboratory. All admitted students rotate in three labs during their first year. After this experience, students settle into a laboratory where there is sufficient interest and adequate resources.